I just updated everything to 4.0.1 moments ago so this issue may have fixed itself, though this afternoon on the previous build, an issue I ran into which, as per the 'use may be another mod, but attacking Covenant for the first raid mission that happened to be fiercely protected with Stealth Assaultrons and a few synth settlers, they became immortal and the raid could not be completed. I ended up redoing the attempt several times with different methods: First redo, I snuck into the settlement prior to meeting the raiding party to first deactivate the Assaultrons and synth settlers but it still would not let the raid complete. On second attempt, moving the synth settlers to another settlement put one of the hud markers at Coastal Cottage to where I sent a synth settler and ended up CTD'ing. Third attempt I removed both the assaultrons and the synths through the workshop completely before meeting up with the raiders which let me progress further into the raid, however, I then had empty indicators in the HUD with 'eliminate remaining' hovering over nothing. I tried looking around everywhere for a hidden settler that fell through the map or wandered off to no avail.
As I do use a plethora of mods, I've included the load order separately to save a bit of space.
As I do use a plethora of mods, I've included the load order separately to save a bit of space.