[nocalora29]

Could you please send a save before you entered said system?, a save which also is like 2+ Jumps away from said system would also be nice right now.

Because the damage is allready done at that save and I can't gather much info, the LOG wants to tell me the whole MQLE Structure has been purged (Saying there are no Quest Label's around at all) and that's pretty devastating.

Note: In the save you gave me I still can happily move my ships around without any problem whats-o-ever.
TL;DR: 1 Save before entering said system, and another one where you are 2+ jumps away from said system.

^^^^^^^^^^^^
That whole post only refers to the second savegame you gave me, still need to test a bit more with the first one.
Sorry for the delayed reply.

EDIT: I just updated MQLE to 1.6, which now enables me to load the entire Structure of MQLE and its QuestLabel environment from a simple .lua File, with that I could re-load the structure of it and the game did in fact work again after using hyperjumps to re-enter the system, but that still despawned the ftu ships.
I still really want to know what would cause MQLE to go haywire like that, hope to see those savefiles soon.