I have a Saitek X-52 with a TrackIR 4 Pro and i had the same annoying problem. Whenever i was playing single or in multiplayer my controllers, especially my Saitek X-52, were disappearing from ArmA 3. I had to exit the game and re-enter so the controllers could be detected again.
I spent several hours trying to understand and fix the problem. I tried the "Power management" untick in the power management of the usb port, i bought a pci-e usb usb. No joy...
I did a fresh install of my Windows 8.1 without any luck. I was really pissed at that time. My last test was to see if Microsoft was the problem so, i went to pick the Windows 10 preview iso and installed it.
I spent two hours flying a chopper in the Sling Showcase mission with the Huron and in a multiplayer Domination mode and never my Saitek disappeared from the controller menu. I went in the controller menu when i was flying to see if i could make it crash again and, no, it was still there.
The only test i have to do is to reinstall my TrackIR 4 Pro and combine it with Saitek to see if the two together can continue to work properly. I think that we're getting close to say that the problem is not ArmA 3 but Microsoft with an unfinished OS....again....
I will keep you posted to let you know if it worked.
Sorry for the faults in my writting. I'm a french canadian who love english.