If the stick isn't plugged when you start ED it clears any binds related to it. As long as you don't save over your binds they should still be there.
I'm on Windows 10, and my controls consist of a Cougar HOTAS and an USB X Box controller which I use for FSS and DSS. Each time I boot my computer there is a chance that the X Box controller is not seen, and if I were to start Elite my bindings would appear to be gone. But as noted above this happens because if Elite does not detect any controller that is part of your bindings, those bindings won't load. Windows sees it, sort of. I think it has something to do with the type of USB it is plugged in to but I don't know. Let me 'splain.
I just stole these images off the 'net, but it shows where you need to click. Notice the X Box controller is shown in the device list
That is what I see, but if I then click "Game Controller Settings" it drills down to this screen
The Cougar always appears. But randomly, it seems, the X Box controller does and does not, appear in this list. It shows under devices (and says X Box controller at the bottom of the screen), but not under game controllers. So I need to unplug and replug to get it to show under this second screen. Sometimes I need to do this several times before it pops. Ignore the 'click on' for properties.
This may have nothing to do with the OP, but I cannot be the only one this happens to, so perhaps it could help someone down the line. As a result, checking this screen is now standard procedure, right after starting Track IR. When all the controllers appear in the second image then I am good to go. If I didn't drill down in Game Controllers to the second image then all appears normal. But until it appears in what the second image shows Elite thinks the controller is not present and my bindings do not appear.