Lock/Protect Files in Mod?

[SvalinnAsgard]

First of all let me say that Mod Organizer is great software. It is very well designed and really helps remove the headaches from modding; I absolutely hated mod managers until I found this one.

 

Now onto the issue. I notice that sometimes, usually after running a tool, some files in mod directories get changed. It makes perfect sense why they get changed as they were altered by the tool, but it becomes really annoying when one runs tons of mods like I do (nearly 200). Ideally, rather than overwrite all changed files in their respective mods, everything would be dumped into overwrite. I tried setting all mod files to read only, but that does not stop them from being overwritten. I also tried putting all mods into BSAs, which keeps the files nice and protected, but the game for whatever reason refuses to load some of them. So, is there anyway to protect mod files from being overwritten?

 

Any help is appreciated, thank you.