That's because you're adding data to the end of the file. If you don't want to reopen file, just truncate it before invoking store_fd.

Update: alternatively just use store and it will rewrite file. So use one of these:

truncate $fh, 0;
seek $fh, 0, 0;
store_fd($data, \*$fh);
close($fh);
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store($data, $file);
close $fh;
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