J-uby, 69 bytes

Takes curried arguments like F[S,B][N].

~:**%(:|%[:& &~:to_i|~:|&(~:/&2.0),:& &~:to_s|~:**&:+|~:%&[:ceil,Z]])

Attempt This Online! (Uses the ** operator that’s missing from the latest version of J-uby.)

Forth (gforth), 105 bytes

: f base ! 0 ?do 0. 2swap >number nip 2drop 2 /mod >r i + r> 0 tuck <# #s 2drop #s #> loop type decimal ;

Try it online!

Explanation

Changes the base to B, then in a loop that runs S times:

• Converts string to a number
• Splits number in 2 halves (one larger than the other if odd)
• Combines the two numbers back into a string

Prints the string when finished and sets the base back to 10 (so we can run multiple times in a row)

Code Explanation

:f                    \ start a new word definition
  base !              \ set the base to B
  0 ?do               \ loop from 0 to S-1 (runs S times)
    0. 2swap          \ places a double-length 0 on the stack behind the string
    >number           \ converts the string to a number in the current base
    nip 2drop         \ get rid of string remainder and second part of double
    2 /mod            \ get the quotient and remainder of dividing by 2
    >r                \ throw the quotient on the return stack
    i                 \ get a copy of the quotient from the return stack
    +                 \ add quotient and remainder
    r>                \ move quotient from return stack to stack
    0 tuck            \ convert both to double-length numbers
    <#                \ start a pictured numeric output
      #s              \ add entire number to output
      2drop           \ drop empty number
      #s              \ add second number to output
    #>                \ convert output to a string and drop number from stack
  loop                \ end loop
  type                \ print output string
  decimal             \ set base back to 10
;                     \ end word definition
    

Japt, 17 bytes

_nW o ó ®ÊsWÃq}gV

Try it online!

Takes input in the order S, N, B with N as a singleton list. Accepting N without a singleton list costs 2 bytes.

Explanation:

_             }g     #Get the Sth item generated by this function...
                V    #...Starting with N as the 0th item:
 nW                  # Evaluate the previous item as a base B number
    o                # Create a list with that length
      ó              # Divide it into two lists as evenly as possible
        ®   Ã        # For each of those lists:
         Ê           #  Get the length
          sW         #  Convert it to base B
             q       # Join the two strings together

PHP, 115 112 bytes

function($b,$n,$s){while($s--)$n=($c=base_convert)(ceil($n=$c($n,$b,10)/2),10,$b).$c(floor($n),10,$b);return$n;}

Try it online!

Ungolfed:

function split_join_repeat( $b, $n, $s ) {
    // repeat S times
    for( $x=0; $x < $s; $x++ ) {
        // convert N from base B to base 10 for arithmetic
        $n = base_convert( $n, $b, 10 );
        // divide and split in base 10, convert back to base B and join
        $n = base_convert( ceil( $n / 2 ), 10, $b ) .
            base_convert( floor( $n / 2 ), 10, $b );
    }
    return $n;
}

Output

B = 10, N = 27, S = 1   1413
B = 10, N = 27, S = 2   707706
B = 9, N = 27, S = 1    1413
B = 9, N = 27, S = 2    652651

2   1   10  11  101 1110    111111  10000011111 10000100001000001111    
3   1   10  21  1110    202201  101101101100    1201201201212012012011  212100212102121002121212100212102121002120  
4   1   10  22  1111    223222  111311111311    2232222232322322222322  11131111131311311111311113111113131131111131    
5   1   10  32  1413    432431  213441213440    104220331443104220331442    12141204110401030043301214120411040103004330    
6   1   10  33  1514    535535  245550245545    122553122553122553122552    131022143412311313533131022143412311313533  
7   1   10  43  2221    11111110    40404044040403  2020202202020220202022020201    40556522600645213204055652260064521320  
8   1   10  44  2222    11111111    44444454444444  2222222622222222222226222222    76650460747555347665046074755534    
9   1   10  54  2726    13581357    62851746285173  3142536758708231425367587081    4861155667688600048611556676886000  
10  1   10  55  2827    14141413    70707077070706  3535353853535335353538535353    17676769267677271767676926767727

C, 245 bytes

int b,z,n,f,r;c(char*t,n){return n?((z=c(t,n/b)),z+sprintf(t+z,"%d",n%b)):0;}main(){char t[99],*p;gets(t);b=atoi(t);f=n=strtol(p=strchr(t,32)+1,0,b);if(!(r=atoi(strchr(p,32)+1)))f=0;while(r--)n=strtol(t+c(t+c(t,n-n/2),n/2)*0,0,b);puts(f?t:"0");}

This isn't going to win anything, but it was fun to make!

JavaScript (ES6) 78 79

Recursive function. Run snippet to test (Firefox only)

Edit 1 byte saved thx @DocMax

F=(b,n,s,S=x=>x.toString(b),m=parseInt(n,b))=>m*s?F(b,S(-~m>>1)+S(m>>1),s-1):n

// Ungolfed

U=(b,n,s)=>
{
  var S=x=>x.toString(b) // function to convert in base b
  var m=parseInt(n,b) // string in base b to integer
  if (m==0 || s==0)
    return n
  else  
    return F(b,S((m+1)>>1) + S( m>>1 ),s-1)
}

// Test
test=[
  {B: 10, N: '0', S:3, K: '0' }, {B: 10, N: '27', S: 1, K: '1413' }, {B: 10, N: '27', S: 2, K: '707706' }, {B: 9, N: '27', S: 1, K: '1413' }, {B: 9, N: '27', S: 2, K: '652651' }
];

test2=[[2, '11011', '11101101', '11101111110110', '11101111110111110111111011'],[3, '2210', '11021101', '20102012010200', '1001212100121210012121001211'],[4, '1113', '230223', '112112112111', '2302302302323023023022'],[5, '101', '2323', '11341134', '31430423143042' ]  ,[6, '120', '4040', '20202020', '1010101010101010'],[7, '134', '5252', '24612461', '1230456412304564'],[8, '22', '1111', '445444', '222622222622'],[9, '4', '22', '1111', '505505'],[10, '92', '4646', '23232323', '1161616211616161' ]
]
test2.forEach(r=>test.push(
  {B:r[0],N:r[1],S:1,K:r[2]}, {B:r[0],N:r[1],S:2,K:r[3]}, {B:r[0],N:r[1],S:3,K:r[4]}
))  

test.forEach(t => (
  r=F(t.B, t.N, t.S), 
  B.innerHTML += '<tr><th>'+(r==t.K?'Ok':'Failed')
      +'</th><td>'+t.B +'</td><td>'+t.N
      +'</td><td>'+t.S +'</td><td>'+r +'</td><td>'+t.K +'</td></tr>'
))

th,td { font-size: 12px; padding: 4px; font-family: helvetica }

<table><thead><tr>
  <th>Test<th>B<th>N<th>S<th>Result<th>Check
  </tr></thead>
  <tbody id=B></tbody>
</table>

Common Lisp - 113 characters

(lambda(b n s)(dotimes(i s)(setf n(format ()"~vR~vR"b (- #1=(parse-integer n :radix b)#2=(floor #1# 2))b #2#)))n)

Ungolfed

(lambda(b n s)
  (dotimes(i s)
    (setf n (format () "~vR~vR" b (- #1=(parse-integer n :radix b)
                                     #2=(floor #1# 2))
                                b #2#)))
  n)

• The ~vR format directive outputs integer in base v, where v is provided as an arguments to format.
• parse-integer accepts a :radix argument for converting from a specified base.

• #1= and #1# (respectively assign and use) are reader variables which allow to share common sub-expressions. When expanded, they give the following code:

  (lambda (b n s)
    (dotimes (i s)
      (setf n
              (format nil "~vr~vr" b
                      (- (parse-integer n :radix b)
                         (floor (parse-integer n :radix b) 2))
                      b (floor (parse-integer n :radix b) 2))))
    n)
  

Pyth, 21 19 bytes

vujksmjldQc2UiGQvwz

Takes input in the format N\nB\nS. Try it online: Demonstration or Test harness

Explanation

                      implicit: z = 1st input (N)
                                Q = 2nd input evaluated (B)
 u              vwz   reduce z (evaluated 3rd input) times by:
             iGQ         convert string from base Q to base 10
            U            create a range [0, 1, ..., ^-1]
          c2             split into 2 lists (lengths are N-[N/2] and [N/2])
     m                   map each list d to:
       ld                   their length
      j  Q                  in base Q
    s                    join both lists
  jk                     join the numbers by ""
v                     convert string to int (getting rid of leading zeros)

CJam, 24 bytes

q~:B;{:~Bb_)\]2f/Bfbs}*i

Test it here. Takes input as "N" S B.

Explanation

q~                       e# Read an eval input.
  :B;                    e# Store the base in B and discard it.
     {               }*  e# Repeat S times.
      :~                 e# Turn the string N into an array of digits.
        Bb               e# Interpret as base B.
          _)\            e# Duplicate and increment. Swap order.
             ]2f/        e# Wrap them in an array and (integer-)divide both by 2.
                 Bfb     e# Convert both to base B.
                    s    e# Flatten into a single string.
                       i e# Convert to an integer to fix the N = 0 case.

ECMAScript 6, 90 bytes

var f=(B,N,S)=>((n,s)=>S?f(B,s(n+1>>1)+s(n>>1),S-1):s(n))(parseInt(N,B),x=>x.toString(B))

Defining a recursive function using a variable is not really good style, but it is the shortest code I could come up with in ECMAScript 6.

Getting the corner case "00" => "0" right wastes three bytes (s(n) instead of simply N).

To try it out, you can use Babel's REPL: copy/paste the code and print example invocation results like so: console.log(f(9, "27", 2)).

Pip, 27 bytes

Lcb:+J[(bFB:a)%2i]+b//2TBab

Takes base, integer, and number of repetitions as command-line arguments. The algorithm is straightforward, but uses a couple interesting language features:

                             a, b, c initialized from cmdline args, and i = 0 (implicit)
Lc                           Do c times:
        bFB:a                Convert b from base a to decimal and assign back to b
      [(     )%2i]           Construct a list containing b%2 and 0 (using i to avoid
                               scanning difficulties)
                  +b//2      Add floor(b/2) to both elements of list; the list now contains
                               b-b//2 and b//2
                       TBa   Convert elements of list back to base a
     J                       Join list
    +                        Coerce to number (necessary to turn 00 into plain 0)
  b:                         Assign back to b
                          b  Print b at the end

Pip's scalar type, which represents both numbers and strings, is handy here, as are item-wise operations on lists; unfortunately, parentheses and the two-character operators FB, TB, and // negate any advantage.

Alternate solution, without the intermediate assignment but still 27 bytes:

Lcb:+J[bFBa%2i]+bFBa//2TBab

Mathematica, 101 bytes

Nest[a~Function~(b=FromDigits)[Through@((c=IntegerString)@*Ceiling<>c@*Floor)[a/2],#],#2~b~#,#3]~c~#&

Uses some Through trickery to apply both the ceiling and floor functions. Just ignore the errors.

Pyth, 29 21 bytes

jku+j-JiGQK/J2QjKQvwz

Really straightforward implementation.

Takes input on stdin in the following format:

N
B
S