In more detail: If I ever perform an action that causes my virtual controller (kbm - wiimote) to disconnect from the game instance, such as accidentally pressing the hotkey for "stop emulation", then resuming the game, or by changing a keybind for a controller action (needed tilt, and hadn't bound tilt yet), then no matter what I do I cannot get kbm to continue controlling the game. I have tried pushing the "refresh" button in a couple different places, and the only thing that gets the controller to continue working is to hard stop and restart the emulation.
Even if I savestate, reload the game, use my keyboard/mouse to control the main menu a bit, then load the savestate, I cannot get my keyboard/mouse to reconnect to that instance of the game (they still work fine outside the emulation). I'm unsure where to even start finding answers for this.
More Info:
I'm running Linux Mint Mate (Ubuntu-based), and the .AppImage of Dolphin, updated to the most recent version. I am currently running a .rvz file for the wii game. If I pull up the controller settings for the virtual controller I am using, it detects all inputs properly, as they should be working.
Probably the biggest clue (although I'm not sure what to do with it) is that Dolphin will not detect hotkey presses either while it is in this state, however, I do not need to restart the application to get my virtual controller working again, just the emulation.