I have something like this hierarchy:

I was in the process of getting all of the project files for work that I had just started and in the middle of the download my computer had crashed. I have some of the files, but I still need to get the rest of the repository. I tried to right click on the head folder to update to get the rest, but it keeps telling me I need to clean up the folders. I have some folders with red a exclamation mark. I tried running clean up, but that wasn’t working. I only had “working copy status” and “Include Externals” checked. I don’t want to click anything else because I’m concerned about messing something up.