UPDATED: Added step 2 which is necessary if you’ve already tried to run ISE as admin once and failed.
Granted that the only problem is the modification of the config files then following steps should work:
1. Log in as normal user.
2. Run “Configure vJoy” and click “Reset all”.
3. Run ISE as an admin user.
4. Remove all files located under <ADMINUSERLOCALAPPDATA>\Frontier Developments\Elite Dangerous\Options\Bindings
5. Copy your .binds files from %LOCALAPPDATA%\Frontier Developments\Elite Dangerous\Options\Bindings to <ADMINUSERLOCALAPPDATA>\Frontier Developments\Elite Dangerous\Options\Bindings. Also, if your .binds file that your are currently using is not named “Custom.1.8.binds” then please rename it to that (working on an update for this as well).
6. Launch game.
7. Exit game.
8. Open <ADMINUSERLOCALAPPDATA>\Frontier Developments\Elite Dangerous\Options\Bindings\Custom.1.8.binds with a text editor (e.g. notepad) and search for vJoy. If you find such an entry then continue to step 8. If you don’t then that means that ISE did not detect the launch of the E:D process which is most likely due to ISE detecting a faulty installation path (out of scope for this post).
9. Copy the files from <ADMINUSERLOCALAPPDATA>\Frontier Developments\Elite Dangerous\Options\Bindings to %LOCALAPPDATA%\Frontier Developments\Elite Dangerous\Options\Bindings.
10. Launch game.
11. ???
12. Profit!
If it doesn’t work. Run “vJoy Monitor” while the game is running. You should see two red axis indicators moving around as you look around on the screen. If this is not the case then try running “Configure vJoy”. If “Configure vJoy” fails to run with an error message along the lines of “vJoyInterface.dll version (x) does not match driver version(0)” then that means your vJoy installation is broken. This is most likely due to conflicting HID-drivers that has been installed on a previous version of windows and are still in use after an upgrade in Windows 10 (also a bit out of scope for this post). If “Configure vJoy” runs fine then that indicates that ISE cannot detect the game launch due to a faulty detected install location.
I hope it works. Thank you for your patience.