When opening projects on Windows with deeply-subfoldered footage and/or extremely long file names, you'll find much of it unlinked, as expected, because it exceeds Windows' (frustrating) limits on file path/name length.
.ai/.pdf files rightfully refuse to relink, telling you that their file paths are too long.
However, most (all?) other file types WILL relink, and seemingly work while you're in the project, only to re-un-link themselves when you close/re-open the project.
I understand this is an unfortunate limitation of Windows itself, but allowing the initial relinking without a warning can allow users to get into some very frustrating trouble, without alerting them to the trouble lurking below the surface.
Even if the relinking is allowed (this *is* very helpful in at least allowing you to make a new reorganized collect, for example), a warning message similar to what an .ai file gives you would be really helpful as a breadcrumb to the user, so they have an understanding of what's about to happen to them. A project with such deep subfolders usually means a LOT of subfolders, and the relinking likely already took you 25 minutes to navigate into each individually (we'll save the comments about AE's lack of smarter relinking for another post).