Saves stripped of mods

[KoreSia]

So I'm playing SSE with around 470 plugins including .esm's .esp's and .esl's and while doing so, I've come across a very odd problem. I can start up the game just fine, open a new game, and go about whatever it is that I want during that time, however when I save my game and try to load it later on, all the mods that I've been using, except for a few .esm's and the .esl's, have been stripped from the save. I'm unsure of what is causing this as it started after I decided to install the creation kit through the bethesda launcher and since then, no matter what I do, or where I save, the mods are somehow removed from the save completely. I realize that I may not be describing this adequately, and for that I'm sorry, but I'm unsure of how else to describe it. When this originally happened, I was able to load back a save from a few hours before it started, but it affected every save made after that time which led me to deleting most of my saves, I then verified the files using Steam, and tried playing again only to have the same thing happen. I've since tried downloading a number of bug fixes and patches in order to find someway to fix this, but I've had no luck. I've used Fallrim tools to examine my saves hoping there was some way of re-enabling the mods that were somehow turned off in them but what I found was that they had been turned into nearly completely useless files except for a select few that I could load up with all my mods and plugins re initializing and a s*** ton of errors because of it. The actual read from Fallrim Tools was: 9598 unattached instances and 343 undefined elements on a save that had around 23 hours of game play. I honestly have no clue what is going on with this stuff and would love some help.

 

I've added two pictures from Fallrim tools, one save apart to show what I mean. I should add that I also use Vortex mod manager.