Updates should have nothing to do with FS9 not working...
EXCEPT
make sure that the FS9.exe is the FS9.exe (no CD), or the 9.1 version, if the sim has been updated,
Maybe copy the whole sim folder from 'Program files' if it is there, & past the sim folder into C:\
Then remane the folder to 'FlightSimv1' for example, & the FS9.exe to FS9v1.exe, for example.
Now you have 2 separate sim installs that will NOT affect each other.
Run the new FS9v1.exe.
This will create its very own FS9v1.cfg & everything should work perfectly.
You can have fun with multiple FS9 installs, for example, have a 'Golden Wings' install.
I have 3x, my third is a Ford Tri-Motor install.