Missing files in Xcode

I'm working with an SVN repository for my Unity project, following these instructions: http://docs.unity3d.com/Manual/ExternalVersionControlSystemSupport.html

At first, I did a checkout at /Users/my_old_path/my_project, but I decided to change this my_old_path to keep the code in, so I just deleted the folder and did a new checkout at /Users/my_new_path/my_project

Now when I build for iOS and open the Xcode project, I get 1071 warnings; one of them is a "Validate Project Settings: Update to recommended settings" warning... I'm also on doubt about this, but my main problem here is:

The other 1070 warnings state that I have missing files, and all of them are something like this:

"Missing file /Users/my_old_path/my_project/some_asset_path is missing from working copy"

I did some research and found something about deleting the contents of the Derived Data folder. I've deleted it but the warnings are still there.

However, I can build and run without apparent issues, but it freaks me out to have so much warnings mentioning a path that doesn't exist anymore, and I don't know if I will have difficulties when uploading to the app store.

Does anybody here knows what's happening and how to fix it?

Thanks in advance!