I think an s///e approach like Tux's s_ger() here is probably best for readability/maintainability, but just for grins, here's a "pure" regex approach: 

Win8 Strawberry 5.8.9.5 (32)  Sun 06/05/2022  5:38:06
C:\@Work\Perl\monks
>perl

use strict;
use warnings;

my $s = 'AAAAAXXXXXXXAAAXXXXXAXXXXAAAA';
print "'$s' \n";

$s =~ s{ (?: \G (?! \A) | (?<= A)) X (?= X* A) }{a}xmsg;
print "'$s' \n";

^Z
'AAAAAXXXXXXXAAAXXXXXAXXXXAAAA'
'AAAAAaaaaaaaAAAaaaaaAaaaaAAAA'

[download]
Please see perlre, perlretut, perlreref, and perlrequick.

Update: And a shameless elaboration: 

Win8 Strawberry 5.8.9.5 (32)  Sun 06/05/2022  6:52:29
C:\@Work\Perl\monks
>perl

use strict;
use warnings;

my %replace = map { 'X' x $_ => 'a' x $_ } 1, 3, 7;

my ($rx_search) =
    map  qr{ $_ }xms,
    join ' | ',
    map  quotemeta,
    reverse sort
    keys %replace
    ;
# print "\$rx_search $rx_search \n";  # for debug

for my $s (
    'AAAAAXXXXXXXAAAXXXXXAXXXXAAAA',
    'XXXXXXXAAAXXXXXAXXXX',  'AXA',
    'XXXXXXXXXXX',  'AAAAAAAAAAA',  'XA',  'AX',  'X',  'A',  '',
    ) {

    print "'$s' \n";

    (my $t = $s) =~ s{ (?: \G (?! \A) | (?<= A)) ($rx_search) (?= X* A
+) }
                     {$replace{$1}}xmsg;
    print "'$t' \n\n";

    }

^Z
'AAAAAXXXXXXXAAAXXXXXAXXXXAAAA'
'AAAAAaaaaaaaAAAaaaaaAaaaaAAAA'

'XXXXXXXAAAXXXXXAXXXX'
'XXXXXXXAAAaaaaaAXXXX'

'AXA'
'AaA'

'XXXXXXXXXXX'
'XXXXXXXXXXX'

'AAAAAAAAAAA'
'AAAAAAAAAAA'

'XA'
'XA'

'AX'
'AX'

'X'
'X'

'A'
'A'

''
''

[download]

Give a man a fish:  <%-{-{-{-<

In reply to Re: Replace all characters inbetween by AnomalousMonk
in thread Replace all characters inbetween by Anonymous Monk

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