Q:

After changing file locations, project can't recognize some of my classes

First off, I know this is a config issue because my code was building and running just fine before I synced my project to GitHub. Xcode's internal source control seems to be having trouble recognizing some of my files and I'm getting Use of unresolved identifier... errors where these files' initializers are in use, and were working before. I'm running the latest versions of Xcode and OS X, and these are the steps I was taking before and after the issue started...
BEFORE:

After several rounds of implementation and committing with the default local repository, I built and ran the app multiple times with no issues.
I created a new repository on GitHub, committed (w/push to remotes) and everything made it to GitHub just fine and was building and running in the simulator.
In order to organize the repository (to match the 'groups' I had created in Xcode) I did some brief research and then added nested directories to my project folder. I re-opened Xcode and repaired the file paths. Some took, but several kept showing ? (although I could still access the code just fine) and I got the corresponding Missing Files... warnings.
Because I couldn't get the new hierarchy to work (the files w/?s, not being recognized, were not able to be committed to GitHub), I tried to move the files back. This worked for most, but for a few (which seem to be the effected files) I had to rename them, recreate a new file and then paste their contents over (this is where I think the problem lies). I was able to commit everything to GitHub (even the problem files went up) but all the warnings remained.
To clear out the warnings I attempted to run my tests, and that's when the Use of unresolved identifier... errors popped up, and of course the build failed. 

AFTER:

I verified all the paths and target memberships were correct.
When that didn't work, I built an entirely new project (although I did add it to the same workspace; not sure if that matters) and copy/pasted all my code over to new files. I didn't drag / reference the files and I didn't link the new project to GitHub. When I went to build, same errors in the same places...
I exited the workspace and opened the new project separately. Still no joy.

Any help or points in the right direction would be much appreciated.
EDIT:

After some help, I tried deleting the reference and dragging the file in manually but that didn't resolve the issue. 
I also checked Build Phases -> Compile Sources and everything was listed fine with no compiler flags. I removed and re-added from Compile Sources, issue persists.

A:

You can try removing referencer for the missing class file in Xcode,then add same file to folder (right click add file ) from physical workspace location this might help.

A:

After rebuilding an entirely new app a third time, with all new files, I copied the files over and this time everything seems to be working fine. Had to repair a bunch of provisioning issues to make sure it worked (maybe that was part of the problem, but I doubt it), but everything is back to normal with the app. The only thing I did differently this time was not adding the new project to the same workspace. 

