Canvas makes duplicate files that are non-existing when existing files exist

What I’m trying to do

Seemingly randomly, my canvas creates a cluster of nodes as “non-existing” when these files do exist. Note how “MOSFET” is a non-existing file attached to “AMPLIFIER ANALYSIS.canvas” in the top left of the image and also its own existing file “MOSFET” that is in the center of the bottom left cluster. This is a also happening for “OP-AMP ANALYSIS.canvas” on the right side. These are notes in the canvas, not references in cards.

It does seem however, that links in the cards also suffer this issue, (the links in common base, common drain, etc… are card with references and they are not linking either.)

Things I have tried

I have tried running in restricted mode, and it still happens. I am not making a bug report as I could not recreate it in the sandbox canvas, but since it happens randomly I am not sure I will be able to. Toggling “existing files only” does not fix it, and the only way to snap that specific node cluster back is to delete a note that is contained within, then add it again. This only fixes the canvas you do this in. Here is my plugin list, but again I used restricted mode and it did not fix it.

Hope somebody knows a solution, thank you!