It sounds like you extracted to the Community folder, then copied from there into the Official folder? If that’s the case, deleting the Longitude files from your Community folder may get it working as the mod writer intended, but having not tried it myself… 
If you just want the default back, the easiest way is to just delete the Longitude files from both your Official and Community folders, then redownload the plane through the MSFS2020 Content Manager in-game. That’ll get you the original layout.json back, in the Official folder.