New bug discovery:
(This post is very important for NMM 0.60.8 and Wrye bash users)
Traditionally good co-working of Wrye bash 3.5 and NMM ceased to exist with appearance of NMM 0.6.+ versions. Example, If you have mods that you manually move up or down in Wrye bash to set up your load order according to your like, and then you run mod merging, NMM memorize those rotations but it cannot properly uninstall chosen mods. It will perform uninstallation, and it will show your mod as uninstalled and removed (if you removed them from your mod list) but, they are still there but invisible. Wrye bash treats them as active and SKSE 1.7.3 didn't record any uninstallation performed by NMM. So what can you do about it?
1. Open Wrye bash and delete uninstalled mods manually.
2. Perform mod merging if your mods were merged
3. Open Save cleaner tool. Load your last save and press "Mod editor"
4. Mark/check mods you uninstalled by NMM and deleted by Wrye bash and press: "Delete created forms" and "Delete selected mods scripts". Save and exit. (otherwise, the game will CTD especially if your deleted .esm file)
5. Load your last save and ignore SKSE's info box about missing mods, save the game on the new slot and exit.
6. Start Save cleaner tool again and press "FixscripInstances" and "Delete all #" if there are files to be removed. Save and exit.
Now you can play your game.