Well, you can, relatively easily...
Once you have created your Custom.binds file by assigning controls to actions (it will probably have 3.0 between the file name 'custom' and file denominator '.binds' which is the version number), you can change the name in Windows.
You will find all your .binds files at /Users/yourusername/Local/Frontier Developments/Elite Dangerous/Options/Bindings
Personally I periodically back up the whole Options folder - just in case. As well as control settings it has audio and graphics settings too.
Once you have renamed the file in Windows, you must now open the .binds file (use Notepad) and change the second line in the file to reflect the name you gave it in Windows.
Here is where you change the name inside the file. You need to modify the three items "PresetName", "MajorVersion" and "MinorVersion" to match the name (and version number) you gave the file in Windows. In my case this was "CustomT16000M.3.0". (In fact you can probably call the file anything you want in Windows, but it makes sense to keep them the same.)
This line is the name the game uses to identify a control setup. It must be unique otherwise the game gets confused, hence why you might set a control binding, and then find that it isn't recognized or remembered if it conflicts with another profile with the same name.
This way, when the game creates a new Custom.binds file, which it will (I think) if you plug in a different controller, your personalized settings won't be overwritten or corrupted.
Hope this helps...
That's what causes this problem in the first place (as far as we can gather).
I would have to do some testing to see if its that or something else that causes it specifically. In the mean time that's all I did to my bindings and they broke quite nicely.
It might very well be the version numbers that didn't get updated along with it that causes it?