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This could be explained if the missing directory is something that would be excluded by the Hidden and Temporary Files file set, for example something like *.old, 'core', etc. Or possibly it's something previously excluded from the project.

Yes, Wing just points to files and directories on disk. You can see the file/dir list in the *.wpr, which is just a text file.

One idea would be to edit that with a text editor while Wing doesn't have it open and remove all the files/dirs listed and then open the project and add what you want. This way you don't lose other project settings.