Hi. Just stuck with the problem after few mods removal (Warzones - Civil Unrest, Crowded Cities, W.A.T.E.R. ...) when scripts still continue to work. Save is doomed with this remaining junk or its possible to clean it?
Thanks in advance.

It is impossible to remove script dependencies, unfortunately.

So then, basically, with every new installed and removed mod, which contain scripts, savegame is becoming more and more bloated with more bugs appearing and someday it will become unplayable?

Yup, maybe one day we'll be able to clean our saves, but don't expect anything anytime soon.

Yep, these orphan scripts are there to stay. Best bet is thoroughly test out a modded setup with a throw-away character before starting a new game. As of patch 1.6 its also better imo to remove any script heavy mods such as WZ, WiS, OCS, SkyTEST, etc, until this issue has been resolved.

The SKSE team may be able to do something about these orphan scripts so you could always post a request in their thread.