I can see a continuous pattern in the data you provided

So my guess why don't you generate the ids right away without reading from the first file ?

Something like this might work???

#!/usr/bin/perl -w
use strict;

my $StartID = '';
my $GenCODE = 'ZZZ';
while (<DATA>) {
    chomp;
    my ( $C , $ID , $NO ) = split /\s+/;
    if ( $ID ne $StartID ) {
        $StartID = $ID;
        $GenCODE++;
    }
    print "$C $GenCODE $NO\n";
}

__DATA__
3998122 CGP_A0000000001 13
5877245 CGP_A0000000001 17
3637488 CGP_A0000000001 19
3998162 CGP_A0000000001 21
638421  CGP_A0000000001 23
2395226 CGP_A0000000001 25
3094278 CGP_A0000000001 27
2029460 CGP_A0000000001 29
1406937 CGP_A0000000001 31
2054853 CGP_A0000000001 35
4182290 CGP_A0000000001 37
3784069 CGP_A0000000002 13
6477860 CGP_A0000000002 17
394789  CGP_A0000000002 19
5095549 CGP_A0000000002 21
692543  CGP_A0000000002 23
5446227 CGP_A0000000002 25
1546807 CGP_A0000000002 27
1741167 CGP_A0000000002 29
1187972 CGP_A0000000002 31
1600142 CGP_A0000000002 33
1833098 CGP_A0000000002 35
1770403 CGP_A0000000003 1353
3254322 CGP_A0000000003 1355
6152600 CGP_A0000000003 1357
3195476 CGP_A0000000003 1361
3108815 CGP_A0000000003 1371
77684   CGP_A0000000003 1373
3269969 CGP_A0000000003 1375
3259137 CGP_A0000000003 1377
6502805 CGP_A0000000003 1379
5899118 CGP_A0000000003 1381
5417394 CGP_A0000000003 1383
806606  CGP_A0000000003 1385
1662014 CGP_A0000000003 1387
6490426 CGP_A0000000003 1389
6206360 CGP_A0000000003 1391
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