If you are using Windows then store the control information in an ADS - "Additional Data Stream". This is just an ordinary file associated with the original. An ADS is identified by a ':' followed by the stream name, for example:

open (my $handle, '>', $filename.':redtape') or die ...
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Perl is happy reading/writing ADS files just like any other.
Gotchas: ADS files are not visible using Windows Explorer, dir, glob, or readdir (see Win32-StreamNames)
ADS require NTFS 5 or later (not FAT)