The problem I had today was that I had added a folder, with source and header files, under 'sources' in the original project When I tried to build the clone, it failed because it couldn't find a new header file that is located in the new folder. At first, I thought this was because I hadn't updated the clone project to include the new folder's path. However, after doing so (I used the 'workspace' relative path, just as the other include paths did), I still could not build for the same reason.
Interestingly, if I right click on the header filename, in the clone source file that includes it, and select 'Open Declaration', it opens the new header file. But building gives the error "no such file or directory". I've cleaned the project and deleted the contents of the output folder. Somehow, the compiler just can't find the header.
So, adding a folder and files to the original project appears to require some other step for the cloned project to build, even though the project explorer show the new folder and files in both projects.
I'm using MCUXpresso 11.2.0.