"Logic Pro X can't recognize file…"

It seems Logic is periodically deleting random audio files from my projects without a trace. The latest incident: I had recorded about a minute of a single electric guitar track and deleted all the old takes I didn't need, only keeping the last take. The next time I went to open the project, Logic got confused and kept saying "can't recognize" audio file after audio file, all files I did not need because I had purposely deleted them. It took several minutes to open the project because I had to click "okay" every time this message came up, but once it opened, everything I needed was still there. The next time I went to open the project, it did the same thing, but when it finally opened, it had deleted 90 percent of my last take, leaving only a few seconds at the beginning. The rest was an empty audio track.

What in the freaking crap is going on here? Is this my somewhat slow, 3-year-old Macbook Pro losing my audio files, or is it a problem with Logic itself? Is there any way to get my files back?

Did you delete the takes manually from a take folder?

Or did you flatten the take folder?

Did you delete the takes manually from a take folder?

Or did you flatten the take folder?

Deleted them in the project, didn't touch the folder.

I may actually be all right now—I THINK it was freaking iCloud Drive somehow trying to ruin everything. I deleted the project and started over. We'll see if it comes up again.