If you are in a mod debugging phase, the best approach is to create a base character without any mod – save it at the beginning of the prison cell tutorial and save it just before the exit of the sewers (in case you want to make changes to the race or class later).
Once the character is saved, reactivate all the mods and do a save outside the sewers – that’s the character you will debug with. Take him/her out for a spin – fast travel everywhere you want to test things – just have fun with it without thinking too much about quests.
Add / remove mods. Change load orders. Install updates. Whatever it takes to fix issues with your game.
And once you are happy with all the changes, trash that character, go back to the save before the sewer exit and start fresh.
There is always a risk to corrupt saved games when debugging a lot of mods. Better to trash the debug character and start over with a clean one.