In FBNeo UI we have an option for this called Clear Locking. Basically, you can "just" clear an input or clear it with "clear lock" checked, and this will make it so that the master preset or preset file never fills it in again. Clear locked input can also be copied into your preset file. I think the SDL version should try to implement this feature.
Clearing an input results in this, in the game's ini file: (let's use the Reset input as an example)
input "Reset" undefined
When it's clear, it can still be re-assigned the next time you load a game using the preset file or "master preset" code in burner.
Clearing an input with Clear Lock checked keeps it clear forever, until you change it again.
input "Reset" switch 0x00
best regards,
- dink