1st, don't worry, the default keyboard settings file cannot be erased in the game's keymapping interface. only your custom keyboard layout can be changed, saved etc.
With a prothrottle + combatstick, u now cannot map the keys onto your joystick using the in game key mapping intereface anymore. That works only for non-programmable sticks, like your F-16 Combatstick when it was a stand alone.
Now you have to first load a template into your joystick using CH Speedkeys programming utility. Any template will do for a start and you can then refer to your game key commands ref chart and remap the keys u want onto your joystick /prothrottle using the CH Speedkeys utility (u have to learn how to use this - quite simple). then save the template as say F18keys or whatever.
note, u can still have a custom keyboard mapped in the game interface to help u get the best combo of keys into your joystick. For example, say in the default game key map the HUD view is Shift F1. And u don't want to have to program Shift + F1 into your joystick. Then u can simply change the game key map to have F1 = HUD and save as custom keyboard. Then program your stick with F1 for HUD and use the custom keyboard in the game with your joystick.
note that the template u use should have at least one button left as A1 or B1 etc in Speedkeys. So that during joystick centering/calibration in windows, pressing that key will be like pressing ENT and the calibration will acknowledge your input. Otherwise, what it reads is really some other key pressed on the keyboard when u press your joystick button that mapped to that key.
i think COmbat Sim Joystick section has some F-18 templates for download for a start. Then u can modify them.
I myself am using a CH Fighterstick, no prothrottle..
cheers and Good Luck..