Here's a tip I have to avoid this issue:
Once you georeference PDFs, go to in "Project Explorer" under "Imported Files" and select the pdfs you just referenced (holding ctrl between them), then go to "Export" > "Construction" > "Trimble Project Link .VCL" and that will export a file that you can use as a backup in case they disappear. It's a band-aid to the problem but it only takes a few seconds and not that much of a hassle.
It may have something to do with the location of the images on your hard drive, is this file saved in any cloud program (Dropbox, OneDrive, Google Drive)? That might be the issue too.