I just had to spend some time recovering a situation when a colleague had inadvertantly started to work offline and had created a load of "phantom" parts.
suppose you pdm vault view is at C:\PDMstandard\
If you work off line the green files all go blue, but this guy didnt notice.
He then created files and saved them at C:\PDMstandard\whatever
Thing is, once back online these files are no longer visible in the explorer at C:\PDMstandard\whatever
This is bevuase they are saved, but not registered in the database. We could still get to them through his recent files list, some of them only as referenced in assemblies that were in his recwent fles list.
Checking in an assembly that had previpsouly been checked in, but to which some of these files had been added, failed to bring up the files - they just vanished out of the assembly in the vault, but were still there when it was opened from the recent files list.
I managed to rescue the situation by saving each file with a slightly different name into the vault now it was back online. Then eventually all the data was in the vault and hunky dory.
So this is a warning, if creating new files while offline place them in a temporary directory and NOT the apparent file path of your vault view. Then check them in at the correct directory location when you are back on line.
Have others experienced a similar issue? what is your strategy for this situation?