Sounds like your company has Pro/MODELCHECK running in batch mode. It tries to enforce certain rules about model construction, parameters, views, layers and a bunch of other stuff. In particular, it adds/deletes layers, moves items to layers, removes items duplicated on multiple layers. It does this unattended, during off hours and goes through any changed files, often in conjunction with the pdm system. If it were available for all users, you'd find it under 'Analysis>Model Check' and you could run your own check and get a report of what doesn't match the criteria set up for checking and which it deems in need of fixing. If they had but a single license and ran it in batch mode, you might never even know they had Model Check.
There is no other functionality, within Pro/e or Intralink, which automatically brings about the changes you're experiencing with layers. It is *not* normal functioning for layers to resist deletion or undelete themselves. Also, other people's def_layer setups in config.pro have no influence on files that were not created on that host as the def_layer settings work *only* when a file is created. It does *not* come along behind you and restore deleted layers: even Pro/GOOFY isn't that goofy! If you'd like to check where, besides your workstation, your files are being altered, look at 'Info>Audit Trail' which shows information from the file header about every hostname that has opend and saved the file. BTW, a checker notating your drawings with Markup Mode shouldn't alter your files or even require saving them. But, while files are at WIP level, anyone in an authorized group can do anything they like with the files unless a pdm checkout procedure is preventing them. Once checked back in at WIP level, they're fair game. Once again, though, this is looking outside the normal functioning of config.pro and def_layer.
Good luck, let us know what you figure out. It's not an easy one, that's for sure.
David Janes