Y15-SUB-B04-P17-BK_M02734_4_000000000-ANNUF_1_1111_24724_4878;size=1;
Y15-SUB-B05-P22-LM_M02734_4_000000000-ANNUF_1_1111_20624_14973;size=1;
Y15-SUB-B05-P22-LM_M02734_4_000000000-ANNUF_1_1103_11326_10379;size=1;

Y15-SUB-B04-P17-BK_M02734:4:000000000-ANNUF:1:1111:24724:4878;size=1;
Y15-SUB-B05-P22-LM_M02734:4:000000000-ANNUF:1:1111:20624:14973;size=1;
Y15-SUB-B05-P22-LM_M02734:4:000000000-ANNUF:1:1103:11326:10379;size=1;

sed 's/_/:/2' old_file > new_file

sed -i'' 's/_/:/2g' file

cat script.awk
match($0,/^[^_]*_/,a){ # match current line to first _ (including) into a[0] variable
   sub(a[0],"");       # remove a[0] from current line
   gsub("_",":");      # replace all _ to : in current line
   print a[0]""$0;     # ouput a[0] and current line
}

awk -f script.awk input.txt

awk 'match($0,/^[^_]*_/,a){sub(a[0],"");gsub("_",":");print a[0]""$0;}' input.txt

<field 1>_<field 2>:<field n>:<field n+1>:...

awk -F_ '{ printf("%s_%s", $1, $2); for (x = 3; x <=NF; x++) { printf(":%s", $x); }; printf("n"); }'

awk -F_ '{printf("%s_%s:%s:%s:%s:%s:%s:%sn", $1, $2, $3, $4, $5, $6, $7, $8);}'

Y15-SUB-B04-P17-BK_M02734:4:000000000-ANNUF:1:1111:24724:4878;size=1;
Y15-SUB-B05-P22-LM_M02734:4:000000000-ANNUF:1:1111:20624:14973;size=1;
Y15-SUB-B05-P22-LM_M02734:4:000000000-ANNUF:1:1103:11326:10379;size=1;

sed  -i "s/_/:/2g" filename

perl -pe '{$n=0}s{_}{++$n > 1 ? ":" : $&;}ge' file

$ sed -e '
     y/_/n/
     s/n/_/
     y/n/:/
' inp.file


$ perl -pe '1 while s/_.*?K_/:/g'  inp.file

#include <stdio.h>
#include <string.h>
int main ( int argc, char *argv[] ) {
  FILE *infp = (argc>1? fopen(argv[1],"r") : stdin ),
      *outfp = (argc>2? fopen(argv[2],"w") : stdout );
  char line[9999], *lptr=line,   this = '_', that = ':';
  int  nskip = 1,  nfound = 0;
  if ( infp != NULL && outfp != NULL ) {
    while ( (lptr=fgets(line,9990,infp)) != NULL ) {
      nfound = 0;
      while ( (lptr=strchr(lptr,this)) != NULL ) {
        if ( ++nfound > nskip ) *lptr = that;
        lptr++; }
      if ( fputs(line,outfp) == EOF ) break;
      } /* --- end-of-while(fgets()!=NULL) --- */
    if (  infp != stdin  ) fclose(infp);
    if ( outfp != stdout ) fclose(outfp);
    } /* --- end-of-if(in,outfp!=NULL) --- */
  } /* --- end-of-function main() --- */