A thought, or rather, a test:
Create a new partition, or even better, grab a new drive, create a reiserfs or xfs filesystem on it, copy the files there, leave them on your system for a while and see what happens.
A guess:
Whatever application you used to download them runs in daemon mode. The files that were 350mb weren't actually complete, as the daemon ran in the background, it continued downloading the files after the client exited.
Cool
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