Hey.

Removing mods is not supported. There are several risks in doing so.

• Game "bakes" (so to speak) script data to save files. Removing the source does not remove this data and Papyrus will create errors, when ever it checks the script for missing source. This will eventually break the game to completely unplayable state.
  
  
• Mod might have masters. Removing a master file for another mod (could be ESM or ESP) will cause the game to crash on Bethesda logo.
  
  
• Game does not actually refresh the world, except for direct replacement edits. These could be textures, meshes or property edits. Leveled list edits do refresh, but it takes some ingame time.

It is hard to say what caused the issue. It could be wrong load order, or incompatible mods entirely.

LOOT (Load Order Optimization Tool) makes a very good job in solving load order conflicts and reporting missing masters. Player still need to patch content between conflicting mods, if conflicts can not be sorted.

Resource conflicts are also important. Resources can be scripts, textures, meshes (etc.)

• Resources packed in to archives (.bsa) load when respective plugin (.esm or .esp) loads. Load order sorting handles those.
  
  
• Loose files will win all conflicts against archived resources. They will "physically" overwrite each other in Data folder. With manual or NMM installation, this is handled by order of installing files. Vortex or Mod Organizer 2 handle these differently, because they do not actually install files in to Data folder.
  
  Resources in Vortrex is handled by mod priorities in Mods view and in resource priorities in MO2 are handled by order of mod folders in left panel .

Your original problems could have been related to wrong load order, wrong resource order or even installing mods that are incompatible between each other. That is really hard to say. I hope this explanation helps you to fix the problem, or rebuild your load order for a new game.