Most mod authors are not going to go to the trouble. esp files, which in that case would have been a major headache. In order to work, all mod authors would need to write their updates in such a way as to be compatible with a simple replacement of. An auto-update feature would be completely oblivious to such instructions. Nexus Mods has now released a new version of their mod manager adds support for Skyrim Special. Vortex has replaced NMM as the official mod manager. The current version of NMM is maintained by DuskDweller and Squidbox on GitHub. The last official version of NMM was 0.65.2. It was declared End-of-Line and no longer supported in December 2016. Even so I'm sure a lot of users ignored the instructions and messed up their games unknowingly. Nexus Mod Manager (NMM) was the in-house modding solution used by Nexus Mods between 20. That update needed a big disclaimer telling users to first click the 'disable and dispell all effects for update or uninstall' button that was built into the mod before uninstalling and updating. Download and install mods directly from the manager. At one point enough of my users had requested a rebalancing of penalties that I decided to edit those effects. Export profiles to easily share both your mods and configs with friends.

Just to provide anecdotal evidence, I made a needs mod that applied penalties via actor effect when you became hungry, tired, or thirsty (which is pretty standard, it ended up being the way New Vegas applied its hardcoe mode penalties.) The way actor effects work though, if you alter or remove the changes they make in an update, it will permanently alter the players stats if they are under any of those effects at the time of updating.

Nexus mod manager updating mods