Maybe I'm seeing this wrong, but why not search and replace instead of backing the file up? So, something like:

open (FILE, "<$file") or die "Can't open $file";
open (FILE_BU, ">$file_bu") or die "Can't open $file_bu";
while (<FILE>) {
   $_ =~ s/search/replace/g;
   print FILE_BU "$_";
}
close FILE_BU;
close FILE;
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Then you could copy (or move) the new file over the old one, or check the result visually and do that manually.

Update: Especially with huge files, I would actually prefer this method over the "my @file = <FILE>" part.