I took a break from playing Skyrim SSE w/MO2 for a few months (last saved game was Feb 15th) and tried getting back into it yesterday and discovered some issues. I was getting an error when running FNIS. After troubleshooting all I knew how to, I eventually uninstalled FNIS and tried reinstalling. I received "No game data on top level" warning even after selecting the data folder in the package which normally resulted in the text changing to "Looks good." I tested other packages and received the same warning. Thinking it had something to do with MO2, I reinstalled. When that failed, I downloaded the latest version. No change.
I went back to Oldrim and MO1 and the game seemed to run fine and so did FNIS. I tested adding a new mod and I am also seeing the "No game data on top level" warning.
I have turned off all of the Windows 10 Game Mode options. Rebooted. Set MO to run as admin. No change.
I am currently on: Win 10 64-bit 1803 (Build 17134.48)