If you don't mind just redoing Solstheim and restarting the dragonborn quest line, there is a solution to this. What you need to do is make a save of your current game somewhere other than in solstheim probably. Then uninstall the dragonborn dlc from your system. Then load that save you just created in skyrim. It will give you a warning that the save contains data from an add-on that has been removed, but all it should do is remove the quests and any items that are exclusive to the dragonborn dlc, which is fine cuz youll do it again anyways. Then after youve loaded into that game and made sure that everything from the dlc is gone, create another save file at that same point so that the game will load that file as one without the dlc at all. Then reinstall the dragonborn dlc and load that save file and just redo the whole dragonborn quest line starting with the cultists approaching you randomly. Make sure you make a separate save after the dlc is uninstalled cuz if you dont and just reinstall it and use the same file, i dont think anything will be different cuz that file will still contain the data for the dragonborn dlc. You still have to redo solstheim and the dragonborn quest line but its better than comoletely starting over or reloading a save from way back.
I had the same problem where I think I fast traveled instead of just following Frea. And, at the time I didn't realize that something went wrong so I just kept on playing the game. So I did a bunch of other things and got to level 40 before realizing I was missing a bunch of the dragonborn quest line. So I wouldve had to revert back to a save a long time ago when I was only level 30 to fix the quest line. Wouldve been a pain to do aalll that crap again. Its much easier to just redo solstheim than like half of skyrim lol.