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Not sure about the answer to your actual question, but here's a suggestion:
Tag the cards somehow to differentiate them (maybe small colored elastic bands that you could slip on as soon as you remove the card from the camera? Or maybe colored/labeled bags that you could put them in)

That's actually a good idea. Pretty simple.

If you are shooting MLV, the camera serial number is captured in metadata. If you are using MLVFS, the SN is displayed for each clip in the webgui, and pretty much all converters will embedded this in the output DNG metadata (which should be readable by whatever post processing app/workflow you are using)

Cool! I'll try it.

I have two 7Ds, time-synced with EOS utility. I'll use the timecode to lay down two video tracks when editing.

My question is, what's the best way to avoid duplicate filenames? I understand it's possible to rename the files once they're on the computer. I'm not 100% confident I'll be able to keep cards from the two cams separate when dumping them, and therefore I wouldn't know which to rename as cam 1 vs 2.

I see the option in the canon menu for image naming. Is there a way to change mlv naming in camera?

Sorry if this has already been addressed.. couldn't find an answer.