Code Inspection Inconsistency

Right now, I have two projects that are the same exact files. In fact, I copied the whole folder (including the .idea folder) and one of them will not lookup methods from Includes, and the other one will.

How is that possible? How can I rectify it?

code_problem1.JPG

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To clarify, I have several of these same projects (some are different branches), but all works except for this copy of the Trunk.

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I had to delete and re-create the .idea directory. Still, I have to have these exactly the same. It would help if all folder specific files were separate from non-folder specific files.

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