It's funny you mention the nebula because in the save I am nearing completion of an Interstellar Relay on a planet inside a nebula, that has to be it, that's why I can save before it finishes completing.
Modlist (Game version 0.9.1a-RC8) :
Lightshow 1.40
Automatic Order 0.3.2
Autosave 1.1
Combat Analytics & Detailed Combat Results 4.6.1
Combat Chatter 1.9.3
Common Radar 2.5
Console Commands 3.0
Industrial.Evolution 1.7.d
LazyLib 2.4f
Logistics Notifications 1.3
SkilledUp 1.1
SpeedUp 0.6.0
Upgraded Rotary Weapons 1.41
Version Checker 2.0
Weapon Arcs 1.3.1
ZZ Audio Plus 1.3.1
The solution seems obvious to me but I don't want to have to do it. My goal with this save is to colonize every planet (maybe leave the core worlds alone for the most part) with an OP pilot using AI cores and the method I've found enjoyable to farm Remnants with is using the Drover spam, I've avoided updating simply for that. I'm pretty sure my Paragon/Onslaught/etc fleet clears faster but this kind of feels like ratting on EVE, I like it. And it doesn't feel too much like cheating (minus being level 103) because this is with Sparks with only one laser and less range.
I tested out if the issue was with Industrial Evolution by cancelling the Interstellar Relay upgrade and waiting for about 15 minutes, it saves like it did before. I suppose from this point forward I will have to avoid building Interstellar Relays in nebulas, who knows maybe I'll get sick of the Drover spam one day and update, I'll probably run into something again that will force my hand.
Thanks for the help!