Deleted plugins are still showing up in editor settings

### Tested versions

v4.6.stable.flathub [89cea1439]

### System information

Vulkan 1.4.328 - Forward+ - Using Device #0: AMD - AMD Radeon 780M Graphics (RADV PHOENIX)

### Issue description

I installed two plugins:
* GodotVim (hmdfrds)
* godot-neovim (shiena)

It didn't end up working out with both plugins, so I deleted their addons entries(folders). Note: I never had them installed at the same time, so I deleted the addons folder for each plugin separately.

Even though the plugins don't show up in the plugins section

Their setting entries, fully interactable, are still in editor settings

### Steps to reproduce

Install either plugin (one at a time):
* GodotVim (hmdfrds)
* godot-neovim (shiena)

Delete the addons folder

Close editor, open editor again. Will see the old plugins still referenced in editor settings.

### Minimal reproduction project (MRP)

N/A