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rename $filename, $filename.".bak" or die "$!";
open(IN, $filename.".bak") or die "$!";
...
}
close OUT;
close IN;

open(IN, $filename) or die "$!";
open(OUT, ">".$filename.".new") or die "$!";
...
close OUT;
close IN;
rename $filename.".new", $filename or die "$!";