Hmmm.

In looking more closely at your regex, it seems like you are replacing a sequence of 3072 characters with a sequence of 1984 characters. Thus if there is one replacement in $block, the statement $final = pack("B*", substr($block,0,$blocksz)); will include 1088 unchecked characters from $block02. That would explain why it appears to be adding whats left at the end of the boundary. You may have to keep track of the number of substitutions performed and then calculate how many characters you need to include in the pack statement. Maybe something like ...

     my $nrrepl = $block =~ s/11110100.{8}(.{1520})11110100.{8}(.{464}
+).{1056}/$1$2/g;
     my $outblocksz = $blocksz - ($nrrepl * 1088);
     $final = pack("B*", substr($block,0,$outblocksz)); # this should 
+work
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You might then have to be sure that $outblocksize is a multiple of 8. It probably will be given the patterns you are working on.

There are a couple of implicit assumptions in the code that we might examine. Is the data you are working with byte aligned and of even size? That is, is the data comprised of 32 bit integers? or does the data vary say, a 4 byte integer, followed by a 7 byte string etc? Since you are packing with 'B*' you could be introducing additional bits at the literal byte (8bit) boundary. If the data is evenly spaced, you could set BLOCKSZ to the size of your regex, that might keep everthing aligned properly.

Another possibility is that when you change a sequence across the boundary between blocks 01 and 02, you introduce a sequence in block02. Your sequence is rather long and involved though so I rather assumed that wouldn't happen but I guess you should consider this as a fringe case.