1 further calrification; it seems as though lightweight components are the real culprit. Even the same assembly, if I open it and a subassembly is resolved (not lightweight) will open and refresh fine in the top level assembly. Once it is set to lightweight, if I switch back, it's hit or miss whether it will appear in the assembly or not.
I have tested a problem assembly on 3 different computers, with fresh installs as well as custom registry setting installs, always the same thing.
Solved. Completely a networking issue (I'm not faulting our network, but I think something has changed in the way SW 2014 resolves components (for performance enhancements)). Working across the network is the issue, working completely locally I was unable to crash or have items vanish after a few hours of intense working with 50+ separate parts open.
Parts are not resolving correctly across a network.