Working on a TW project last week. I am actually the only one accessing the TW file currently, so I know no one else was in it messing around. When opened Monday AM all layers are gone (our typical office standards from template) and have been replaced by five layers seemingly from the Custom Profile Manager somehow, see attached. All objects in the file show layer as MISSING. All layer combinations from template are still listed and have random impact to the five "new" layers.
I was able to go into BIM Server Mgr and Download the saved PLN from Friday and all was fine there. The PLN was saved when I last did a S/R when I closed out on Friday. I was able to re-share the saved PLN so I'm back to where I was but this is a very weird and potentially problematic issue. Thankfully it didn't happen at the normal time when these things do, Friday evening, at a deadline with multiple users on TW and no one here to fix it.
Kevin, a few clients of ours have already reported similar problems. Such might happen if you have the complex profile editor open, the layers settings reserved and ArchiCAD crashes. When you re-open the autosaved project, all standard layers will be replaced with the complex profile layers as that set of layers was active previously.
Our engineering team has successfully addressed this, so the upcoming hotfix (build 3482) is going to include the complete solution.
Until the hotfix arrives the only solution is to roll back to a previous backup.