I used Adept a few years ago at a previous employer. I do not remember any specific problems with it, but I didn't use it for very long before leaving that organization.
This may or may not be directly applicable, but in my current PDM system I have seen this behaviour when the file locations for 'referenced documents' wasn't set to include all the locations the PDM program might put the files (for my system, that's four directories a file could reside in depending on its status). If one of the file locations isn't set, and that's where a referenced file is, it will get suppressed (or hidden if it's a drawing view that can't find a reference). This can happen at any point in which the files status are changed, and the suppressed/hidden state will be saved the first time it can't find something and won't automatically unsuppress/unhide if it can find it later in a future status.
When you open a file and SW cannot find references, SW tells you and prompts you to relocate it. When my PDM system does opens/closes files automatically as part of the status change process, this warning message is suppressed, so you don't know something has gone missing until you try to open it later.
