I just started the game, made the tutorial using keyboard/mouse and then decided to give my T.16000M + Throttle a try and loaded that configuration. Quickly I decided to go back to keyboard/mouse as it seems to give me better control over the vessel. But now all control prompts in-game are joystick buttons (B1, B2, ...).

I tried loading the Mouse + Keyboard settings from the control options, but when selecting that entry, the apply button stays greyed out. I tried loading a controller setting, hoping that would switch the prompts to Xbox or DualSense images, but even with loaded controller config it's still joystick button prompts. In the general game options I changed the button prompts to Xbox and DualSense. No changes. I tried the override option multiple times with different settings, but I still get joystick prompts.

Any help regarding this?

I just found out myself. In the control options, there's a menu entry delete all settings which will do exactly that. After applying that setting, it's possible to load the default settings and the prompts are back to normal.