This had been happening not in just one project but a number of projects. (ie the reason I did not include video codec and sequence settings). In talking with a FCP expert here is what our best guess at the problem has been.
Because some projects had been edited using Sony xdcam raw files. Our system was being over worked trying to adjust/ process on the fly. When a sequence was started and it asked to conform sequence to footage I said yes. That resulted in the more than occasional unexpected quit, when that happened some metadata did not get written, so while a project would look fine on re open and restore, on out-put it would refer to an earlier render file.
So here is our solution.
1. Full delete of render files, and “all of our fav” trashed the preferences.
2. All footage is now imported, batched, and edited in pro-res 422 (sometimes HQ) sometimes regular.
Thank you all for insight and help.
Stasia