Nope, doesn't work that way...
You can copy out a "valid" BINDS file and re-copy it back, but simply launching the game, or selecting the config menu will erase all the bindings. ("erase" is really the wrong term here, since the bindings are in the file, the game just chooses to ignore them!)
It's now a one-shot deal; re-assign all binds and be damned sure you get it right, or you need to do it all over again! But, you'll still have to do it all over again if you quit the game!
This is why this is a critical issue!
Note that the X-55 is TWO completely separate HID "game controller" devices, the stick device is completely unaffected in the controls menu. Only the throttle unit is affected with this bug.
I'm sorry, but as an X-55 owner, I don't have this problem.
1 - set up the binds, if you change anything from the standard X-55 set up, you are now using "custom.binds" file
2 - copy the binds file "custom.binds" to a safe place.
3 - for ease of use, rename file to something like "myx55.binds"
4 - IMPORTANT: open the binds file in a text editor (it's an XML file), there is a line two or three down where you change the text string from "custom" to "My super duper controls"
5 - copy back to default binds location.
6 - there is now an item in the list of configurations called "My super duper controls", when you enter options/controls, load this after every update
EDIT: I also have the MadCatz software installed, if that makes a difference, but I don't use the programming part of it