After a closer look, I notice you have ($newbase = $base) on both conditions of your tertiary. My first thought was instead, my $newbase = $base;.
But, you only need $newbase if $base matches the pattern. Further, you stop using $base; you may as well make changes to it rather than $newbase.
So, perhaps this:
...
for ( @found ) {
my ($base,$dir) = (basename($_),dirname($_));
next unless $base =~ /$pat/;
defined $opts{n} ? $base =~ s/$pat/$rep/
: $base =~ s/$pat/$rep/g;
my $newname = File::Spec->catfile($dir,$base);
if (-e $newname) {
warn("can't rename $_ to $newname: $newname already exists\n");
} else {
rename($_,$newname) or warn "can't rename $_ to $newname:$!\n";
}
}
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