I've never heard of this...

When I capture files, I keep them in the job folder and have no other place that I store them. Even so, I've been revisiting nearly completed jobs and it asks me if I want to search for such and such file. I do, and look throughout every hard drive I have. Nothing. So I ignore it, open the M2T, and see 'Media Offline' where the clip used to be in the timeline. After four jobs with this happening, I cannot imagine this is a coincidence, and I haven't deleted any files in this time period.

Thoughts?

Are these files visible to windows?

No, they are nowhere. I've heard of a virus that does this sort of thing...

Are you using a firewire or usb2 drive by any chance? I've seen that happen on a friend's mac... the file will re-appear I think.

2- Other things you can try:
Check for viruses by doing an online virus scan.
Run a program called Hijack This and run the logfile through hijackthis.de
*Hijack This may get false positives / negatives... I would not make changes to your computer unless you are 100% sure, or get someone to help you. There are various getting rid of malware forums on the internet.

3- You could try to see if data recovery programs pick up your files... e.g. Active Undelete. (This process is slow.)

It's on the main drive of the computer.

I tried data recovery...I'll look into HijackThis...

Thanks