As neoxed told you, this is rather the pretime script's job than the autonuker's.
You mention a pretime bot in your first post which means you would have to link the sitebot and the autonuker.
To achieve this, the sitebot would have to watch the channel activity and log to a file (ie. ioFTPD/scripts/autonuker/backfill.dat) the dirs that have to be nuked. The next time the autonuker is called (every x minutes), it would also check this file to see if there is something it should nuke.
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