Apparently, using that "load 3" in the levels for enemy/npc type entities causes the engine to close randomly. I was only able to understand the relationship because I'm using GitHub on SORX and I was able to draw a timeline of when this problem started. After several tests, I realized that it was after I added "load 3" to the enemies, and after removing it, I had no more problems.
About "load 3" I also don't have many details, but from what I understand entities with an A.I. more complex type enemy/npc at a certain point the engine gets lost when unloading/loading and ends up not finding it to spawn in the levels. I've never seen it happen with panels, items and obstacles, so much so that I use load 3 on them straight away.
To be honest, I even have some npcs using load 3 (like the manhole cover on the first level of sor2, it detects the player and lets Donovan leave) but they are only used for decoration, I believe that due to having very little stuff he doesn't causes a problem, but in the case of my cpu partners, which are npcs working almost the same as the players, this crash happened directly with load 3.
I don't see where we could be going wrong in using these features. Unless Damon has some additional information, in fact both are engine issues.