Everything checked out ok with the searches, in other words everything looks ok
You shouldn't search anything. There are just to keys in the registry that contains the FSX path, and they should contain ONLY the path, not the whole filename including FSX.EXE
The key used by GSX to look for the FSX folder, is this one:
HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator\10.0\AppPath
And it should be (in your system) like this:
E:\Flight Simulator X\
and NOT like this:
E:\Flight Simulator X
or, even worse, like this:
E:\Flight Simulator X\FSX.EXE
But if it has gone away now, perhaps you had a product that touched it temporarily for some reason, then it went back to normal again.