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open(OLD, "< $old")         or die "can't open $old: $!";
open(NEW, "> $new")         or die "can't open $new: $!";
...
close(NEW)                 

rename($new, $old)

open(OLD, "< $old")         or die "can't open $old: $!";
open(NEW, "> $new")         or die "can't open $new: $!";
...
flock (NEW, 2);

[continue as before including renaming the file before the filehandles
+ are closed]