I am not sure if I completely understand your problem. I try to replicated:
1. You change bindings they get lost.
2. You want to use the thumbsticks to control your thrusters.
3. You want to use the slider on the throttle to switch to reverse.
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On point 1: Do bindings only get lost when you change something? If yes, can you please give more information on what you change, possibly even with a video on how you do the changes?
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I see two mist likely problems:
- For whatever reason (e.g. some bug in the installer) your configuration file is set to read only. This would mean that the game can not save the changes and resets to default values again and again.
- You make a mistake in doing the bindings and somehow manage to overwrite some of your already created bindings. Due to the huge number of possible bindings and due to some of them seeming to be very similar in this game (but actually having quite different results in gameplay) this is more likely than you would expect.
On point 2: This is actually the default setup for the X-56 in Elite Dangerous, but you might want to arrange them differently. To do that, you have to go to your controls, to the section "thruster override" (or something like that, I don't have the game at hand right now). There you can bind buttons or the thumbsticks to the directional axes. Make sure to not bind your thumbsticks to the button bindings, else you only have the option of "full thrust" or "no thrust", but rather bind it to the axis itself. (Then try in a tutorial if it works like expected, don't do testing with your valuable ship. ) Depending on what you bound, it might be necessary to switch it to reverse.
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On point 3: Using the slider in Elite Dangerous is a little tricky, but i figured out how to get it to be used. Mind you, I have not tested if Elite Dangerous now recognizes the slider of the X-56, but for sure it did not recognize that of the X-55. When I migrated (as my X-55 broke down and was returned on warranty) I did not test a change, but just immediately used what I know that it is working.
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Steps to get it working:
- Use the programming tool for the joystick to bind a key to the slider. I used the pause button, as that one is not used anywhere else and does not create problems even when I forget the slider in the on position. (I started with it being bound to Alt, but soon had to notice that this of course triggered a number of key combinations and thus was a very bad idea. )
- Go to the throttle section in the games configuration menu.
- Bind the same button to the reverse option there.
- If the binding is set to "toggle", change it to "hold".
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Then the throttle will be set to reverse as long as the slider is being activated, and your ship will fly forward again when you move the slider to the "off" postion. (Mind you, i use the slider in a different way, though. I use another key to toggle reverse, but have flight assist off on "hold". One button on my joystick is bound to flight assist off, and the slider on the throttle is so, too. If i want FA OFF for just a moment, i press the button on the joystick for a quick turn, if i know that i want to stay in FA off for a little longer, i move the slider on the throttle as it keeps the key pressed by itself for as long as i want it to. )
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I hope this helps. If it does not, please give me more information on your problem.
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A small addendum on the binding: yes, using the MadCatz software unfortunately requires you to save a profile and manually reload it every time you restart the computer. I have not found the option yet to make the software automatically load the configuration again after reboot.
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If somebody knows a way to make that happen, please let me know.
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That being said, i very much advise to use such a profile, anyway. I found it very useful to bind several energy management presets to the two 4-way switches on the throttle, so i just move one of them into one direction and immediately have the energy distribution i want. It's much more convenient than the default "down-left-up-up-right-right-enter-Nintendo-code" default method.

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