So during my timelapse I needed to edit a couple of the raw CR2 files (people needed to be taken out of a few pictures) and I'm wondering if there is a way to make LRTimelapse work with these edited pictures?

No, I'd not recommend doing so. I'd rather make the individual edits on the intermediary sequence after exporting from Lightroom. After your edits you can then use the LRTimelapse renderer the render the sequence via file/render video. Just select the edited intermediary sequence in the dialog.

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