just adding an s modifier to each regex ought to do it: it'll then treat the whole thing as if it were one line (or, strictly, it'll treat line-endings as just another character), as the early parts of perlre will explain. I should have put that in, but your example was just one line so I didn't bother:

$test =~ s/(\\\*.*?\*\\)/ push @comments, $1; '%%comment%%' /egs;
$test =~ s/\\//gs;
$test =~ s/%%comment%%/ shift @comments /egs;
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