I'm Faced with the same issue. It appears that something went wrong in the repository.
I was able to recover the app by looking up the ObjectID in he same log where the error is reported. This ID appears as a hash key and corresponds to a filename in the directory <C:\ProgramData\Qlik\Sense\Apps\>. When copy this file and rename it to <FileName>.QVF you can import it into Sense.
The file should preserve the last moment when saving or reloading.
Because I saw the same issue with the same software version (3.1) I'm afraid this is not an incident, although I really hope it is.
Unfortunately this was not possible since the repository service could not find the App.
But, I have done some research in the meantime. This issue re-occurred in the afternoon when I restarted the Sense services. What I think what happened is that the Repository service thought the app was still open in a session while it was not. A restart of the services made my initial Apps available again but gave the error when opening the imported copy. For some reason this imported app was stored in the default app location but because I changed the app storage location in the engine properties the repository was not able to find it.
Check the settings for your <app storage location> and look for the physical file in this location. It might be stored somewhere else and copying the file will solve the issue.
I submitted my case to Qlik. They analyzed my log files and found the the issue probably lies with the amount of installed SSL certificates. Apparently I have 350 certificates installed and Qlik Sense "Might show unexpected behavior" when confronted with more then 300 certificates.
The issue has not occurred since the last time I posted here...