sorry for my naive suggestion, infact is not at all my field (well.. what is my field? ;) but what about something like:

use strict;
use warnings;

my @str = qw(
    ABBCBCAAAAABBCBCACCCAAAAACAAAAABBBBBAAAAABBAAAAAAAABBCCCACCAABC
    BCCCBCAACAABBBCAAACCAAAAACAAAAABBBBBAAAAABBAAAAAAAABBCCCACCABBC
    ABCCBBBAAAABBABCACABCCCCCCAAAAABBCBBCCCCAAAAAAAAAAAAACCCACCACCC
);

foreach my $str ( @str ){
    
    print "$str\n", 
            $str =~ s/([A-C])(\1{2,})/$1.(1+length($2))/reg,
            "\n\n";
}

__END__
ABBCBCAAAAABBCBCACCCAAAAACAAAAABBBBBAAAAABBAAAAAAAABBCCCACCAABC
ABBCBCA5BBCBCAC3A5CA5B5A5BBA8BBC3ACCAABC

BCCCBCAACAABBBCAAACCAAAAACAAAAABBBBBAAAAABBAAAAAAAABBCCCACCABBC
BC3BCAACAAB3CA3CCA5CA5B5A5BBA8BBC3ACCABBC

ABCCBBBAAAABBABCACABCCCCCCAAAAABBCBBCCCCAAAAAAAAAAAAACCCACCACCC
ABCCB3A4BBABCACABC6A5BBCBBC4A13C3ACCAC3
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L*