if they are not uploaded to your ftpd, then they won't trigger any script inside io. If they all go to the same folder you maybe could schedule a rescan of that dir evere hour or a time you like. For that you need a zipscript, that supports rescan of a dir.
Only issue on this one: most zipscripts only check one sfv per dir. You would have to keep the dir clean after a rescan is done or you just would have to trigger the rescan on your own manually.
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I'm using:
ioFTPD 7.7.2
ioNiNJA BETA Stable v0.8.9.6
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