One problem you have is that you're recompiling the regexes over and over again. Better to cache them. I'd do something like: 
# Preprocessing phase.
my @subs = map {my($r, $s) = split /\t/; [qr/$r/, $s]} @Patts;
# Real stuff.
open(my $in,  "<", "...") or die "...";
open(my $out, ">", "...") or die "...";
while (<$in>) {
    s/$_[0]/$_[1]/g for @subs; # No need for /ee, is there?
    print $out $_;
}
close $out or die "...";

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In reply to Re: Massive regexp search and replace by Anonymous Monk
in thread Massive regexp search and replace by albert.llorens

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