A user reported this to me once a few months ago. But, I haven't personally seen it. Played around with a number of things to see if I could reproduce it. But, didn't have any luck.
The most relevant questions would be related to the interoperability of the various programs, and the actions that were taken between the last save (when Foundation data existed) and the newest save (when the Foundation information was discarded). If this has happened multiple times, then if you could remember any pattern to the behavior that you can give to us in Tech Support, that would really help.
If this was a Floor-3D-Foundation model. Obviously, if you save in RISAFoundation, the foundation information will be remembered. But, if you go all the way back up to RISAFloor and save, could there be a way to get the Foundation information to not be saved. I'm thinking about a particular RISAFloor feature that allows you to delete all RISAFloor based members from the RISA-3D model. This is done to be used when you leap frog floor levels over other existing floors. That can cause great confusion with existing walls and columns. So, it is sometimes easier to just force the program to recreate them in the 3D side of the model. Well, I'm thinking that if this feature were used, it might also delete the Foundation data too.
I'm not in the office, so I haven't gotten a chance to test it. And, I know I didn't think of that feature when that previous user contacted me.