Another update: I tried this a bit more extensively, it’s pretty good because you can get the GI to always load the level you’re working on, with a bit of fiddling
and then in the persistent
The only level instance that failed for me before was a lift. I managed to get this to happen again, and discovered the lift was actually elsewhere. Is this possibly happening with your instances? ( really depends on how things work with you ).
Another update ( I give up 
): I can get this to regularly not load a level instance, there is a pattern. If I’m editing level X, which contains code to load level Y, and press play, level Y will not load. I think what is causing this is
1 Level X has code to automatically load level Y
2 PIE loads X ( because I was editing it ), which starts to load Y
3 Open level opens the persistent
4 Persistent reads that I want to stream X and starts re-loading it
5 X now, again, attempts to load Y, but Y is already marked for unload since the ‘open level’
6 We end up with no level Y
Indeed, delaying the stream of level Y, did the trick…