Steve
I've run into this before, and I'm pretty sure what it means is that PI can no longer find a certain swap file that is needed in order to create the project correctly. If PI runs out of swap space, it starts to throw out the older files to create space for new ones (more or less). If you go too long without saving, you run the chance of the program throwing out something you need, as you experienced. The only way forward, I think, is to delete the file that is associated with the swap. Then, you can save the project minus that one file. Once you get burned by this issues once or twice, you will learn to save your project at the end of every processing session. Since it now only updates changed files, it only take a minute to run, usually.
Mike
If the above info is wrong, someone please correct me.