Recently we had an issue where the Qlik database was out of synch with the Qlik application do to a change we made. I see something similar now where I have created an APP and then the next day when trying to access the APP it gives me the error, "The APP you specified could not be found". However, the APP is showing in the HUB, and in the QMC.
What I notice is that all my accessible APPS have "App Contents" with File Names, Location (referencing %RepositoryRoot%), URL, and file sizes. The APPS I cannot access do not have any "App Contents" showing.