I have a quest in a mod and a save game that has seen that quest. I added a scene in that quest that doesn't automatically start and that save loads well and that scene starts if I do what's needed for it to start.

Now, if I go back in CK and only edit that scene (add/remove phases or recompile fragments) and save the esp. When I go back in game and load the same savegame the game crashes immediately after load screen. Once or twice I had the chance to see for a couple of seconds some NPC freezed and others animated before the CTD...none of those were related to the scene and also the scene wasn't even started.

The CTD happens every time I try to load that save and seems to go away if I also edit something else beside the scene in that mod and save the esp again. So, to me it seems like some sort of esp corruption if I only edit a scene between CK saves.

Anyone had similar experience? Any idea what exactly is causing this and should be avoided?

Load a save from before the events were triggered for that scene. Even if it means going back and restarting the quest. See if that works.

Saves get a lot baked into them from mods, so changing a mod on a save is not a good idea, even if, or especially if, it's a mod your editing.

That game save isn't made after the scene is triggered, it is true that it has seen the quest but it loads fine after I add the scene to the mod. I tryed meanwhile with a save that didn't seen the quest at all and it just occasionally crashes....unfortunately my mod is also already published with that quest I want to enhance it.