Have you done an independent check of directory contents
before and after a given run? E.g. if it runs at 09:00,
you should do a (gnu) "find" (or something equivalent)
on the target directory a couple
minutes before execution, and again a minute or so after
execution.
It may be that having %Dir tied with IO::Dir, while trying to
modify the contents of the target directory, is causing
unexpected side-effects (or failure to behave in the expected
manner), and the problem is not with the @FileList array,
but rather with the directory contents.
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