I have no idea why restoring the original GVP file is not enough to fix the issue, but you can use Steam to make sure you have the correct file.
To do this, right click the game from the Steam library and select Properties. On the "local files" tab select "Verify integrity of game cache". It will revert all files that have been modified though, there is no way to select the gvp file only.
EditVoicepack will look for Prepar3D.exe in the folder - if it is present, it will identify it as a P3D installation. I can't say of SKYAI puts a Prepar3d.exe file in the folder.... it would be a pretty strange thing to do.... but then, strange things happen.