How about one more layer of error checking, on the chdir command:

chdir "/home/main/sub/newfiles" or die $!;
open(WRITE, ">$file") or die "Can't open $file: $!";
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That is, just because the program runs, doesn't mean it's working correctly. It's possible that the chdir fails and the open is creating a file in the current directory. It's worth checking, anyway...

buckaduck