I've lost all my Palm Apps from GVM a few time now. I haven't found a consistent chain of events to induce this. I wasn't doing what you described above either. The only thing in common is that the app I was running crashed and when I went to launch GVM again - all was gone except the stock apps. Once this occurred when running an app without GVM running (ie: launched app from command line) and twice with GVM running.

It sure is a pain that if you get a little instability in one part of the GVM.store file it appears that it wipes the whole file. It's also quite a pain to reinstall everything. There is no magical way to make them retinstall themselves.