Illustrator File Bug spreading...

Not sure how it happened. I have two files... a PDF and a document in illustrator I'm working on. I placed the PDF in Illustrator file I was working on to trace it. I had to make a change, so I opened the PDF itself and edited the file. When I saved the PDF I was prompted with "Some files are missing or modified... now?" So far so good.
When I was done tracing the file, something happened in the PDF file (which was still open in another window) which caused the timestamp to be changed on the file. Could have been Windows (I've seen this behavior before.) could have been an automatic backup... I'm not sure. I made no changes to the file.
I hit "No" do not update, because I was planning on deleting the layer I traced. Next I deleted the layer. Then I am prompted with the update links dialog when the links palette is empty. I dismissed it, closed the file, closed Illustrator, and went about my day (yesterday).
I had to open the file again today for editing and the message came up again. After I closed the file, now it's happening to other files which have no links either. (I closed the original file with the issue.) It's a bit of an annoyance because it prompts me every 60 seconds or so to update the links in the links palette. If there are links in the links palette (for a different file) it does not prompt me, but when links are non-existent in the file I am prompted. The screenshot is from a completely different document after the corrupt file was closed.
There are no symbols with embedded links or images and no raster content (with the exception of a couple of non-expanded blur effects exist. If I open a different file, after restarting illustrator, everything works as expected until I open the *corrupted* file. Then the pattern begins all over.
For my workflow, I normally work in native AI and save those files with un-outlined fonts (for editing) then I will finalize a file by converting it to outline files prior to saving to EPS. Sometimes I will save a proof out as a PDF if the file I'm working on isn't imported into something else. I'm not usually in the habit of importing PDFs for tracing in Illustrator, but I was in a hurry and figured it would work. It placed it, but now it haunts the document FOREVER.
Thought I would share.

That's definitely a good troubleshooting method to go about solving an issue with a corrupt file.
Reimporting the PDF in my case did not fix the problem because the phantom  PDF does not exist in the form the program is searching for. Despite having another version of the file linked, the program knows the *embedded* PDF that was not removed has been updated in link form and it tries to update the non-existent link.  I say embedded because AI tries to save PDF compatible files natively, so it embeds links even though it still maintains the linking in the links palette to allow people to update changed files.
Copying the selected content from the file to a new file was the first step I took to fix the issue I had. When my client referenced the older proof I reopened the old file and that's when all of the trickery began for Illustrator itself, causing the program to treat other files as if they had missing links long after the corrupt file was closed.
On another weird note, the phantom placed PDF still shows in a saved copy as a PDF (with a PDF extension) on Apple's preview app on iOS and MacOS.
My client thought it was a design element when she viewed the proof on her iPhone and was giving me changes per what she was seeing. The file does not appear this way in Acrobat Reader or Acrobat Pro.

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