I have the same problem.

I had it previously with a CH Combatstick USB and CH Pro Pedals USB.

Now, occurring with Thrustmaster HOTAS Warthog joystick, Thrustmaster HOTAS throttle, and CH Pro Pedals USB. Was connected via individual ports, or by a USB hub.

TrackIR is not affected at all.

When I lose the joysticks, unplugging and replugging within the game does not allow the joysticks to show up. However, if I quit Arma 3, unplug hub, replug, and re-load Arma 3, the joysticks appear again. However, I might lose the joysticks 10 minutes later. This makes consistent multiplayer gaming nearly impossible if I have to quit and rejoin just to have my joysticks back.

I heard that there may be a capacitor issue with the USB ports on the motherboard, but have not been able to find more information about this.

It seems like the problem occurs with great frequency if I go to the options menu while playing the game.

I can confirm that the bug affects my controllers in the Altis Map, but NOT the Stratis Map.

Happens in both singleplayer and multiplayer.

Steps to recreate:

1. Open ARMA3
2. Start ANY mission
3. When mission is loaded and player is in game, open settings, controls
4. Thrustmaster Warthog Joystick and Throttle and Saitek Flight Pedals disappear, do not work in game any longer. TrackIR is still working properly.
5. Quit game.
6. Restart game and start any mission.
7. Controllers all working properly.

Windows 8.
ASUS ROG G750 laptop