Go to the product menu, and you will see the Clean
option.
Now, hold down the option
button on your keyboard and the text should change to Clean build folder...
Choose that option, and it will additionally delete the derivative data folder that caches alot of things including the texture atlas, and I've found to cause problems like you have described. If you rename files in the atlas, thats typically when I have experienced this issue myself.
I don't like that this option is something you kind of have to work for, would be nice to have this second option there WITHOUT having to hold down the option key.
If this doesn't solve the problem, you truly have a naming problem imo.
Note You can also delete the derivative data folders from the Organizer window.