I'd like to preface this by saying that I've modded the $#@! out of CC, so I may have goofed something up along the way. But:

I tried uninstalling CC24 so I could make a new area for 25 to come in, and then I figured I'd re-add my repository of mods after 25 was installed. However, I noticed there are several files that I am not allowed to delete, namely the .exe for CC proper, as well as a few other tiny ones.

So I installed CC to a completely different path instead, but it wouldn't work. I assumed this was because of conflicts with the remnants from the old install, so I tried uninstalling the new one, and the same thing happened, with the same three files hanging on: Cortex Command.exe, fmod.dll, and libcurl.dll. I'm not allowed to delete any of them because I don't have "permission"...

Also, I have the CortexCommandModManager, which won't run anymore because it insists on loading the now-deleted .ini file from my old install path. I suspect the two problems are related, but I'm so confused right now I'm scared to touch anything else.

Any help is appreciated, even if it's just a way to delete all that is associated with CC from my computer. I'll happily re download everything if I can just get the game working again.

Have you tried restarting your computer?

Usually when this happens the file in question is still in use, as in, running.
Try opening the task manager and looking for Cortex Command.exe under the Processes tab, then click End Process.

If all else fails, try rebooting?

I did a system restore and while that straightened out the dumb immortal files, CC has still decided not to work. Now it's dumping me during the loading screen, saying some such nonsense about "abortion from .\Managers\FrameMan" or something. And it mentions line 481. And a file named palette.bmp that is supposedly in Base.rti even though it is not. I have searched for it and found only a shortcut to a file that doesn't exist.

All of this has me quite confused because it seems to have happened out of the blue, seeing as how I did the system restore. A vanilla install isn't working either, now.