Yeah, if there is a disconnect, I think the universal ramification of that is that you cannot get control back for any online game.
But there is no reason why you should get the brief disconnect and then reconnect, if there is no battery or USB issue.
If you know the batteries are fine, the USB port/controller is fine, and that the controller itself is fine, then I'm afraid I'm at a total loss as to why you're experiencing this.
I've been playing with the same XB 360 wireless controller I used for 2K16 and have not had any issues except for the known battery-died-disconnect or the same problem occurring because I forgot to have my controller on when I launched the game.