Two potential reasons for this to happen that I know of:
First one is, you should rename your own custom settings with a meaningful name, so it doesn't just look like "custom". So whenever an update actually defaults to "custom" you only need to pick your renamed settings from the list.
Second one is if one of your devices is somewhat shaky and not always recognized by the game (here it's my head tracker that needs to be replugged on each reboot to be recognized, most likely a buggy USB module on my outdated motherboard). Whenever I forget to re-plug, my whole setting falls back to "custom" (in this case my renamed settings don't even appear on the list) - which of course is totally different from my (renamed) own custom file. In which case I only have to replug my device and now can pick it up from the list again.
Whatever, I doubt it's actually the game's fault but the confusing variety of possible devices that requires a little bit of 'handiwork'.
About half the times it's happened to me, keeping a backup has proved fruitless, as it's identical to the one the game can't load and so doesn't get loaded anyway, defaulting back to mouse and keyboard.
After 3.0 dropped there was absolutely no getting around this and I had to remap everything from scratch. The most recent time it happened was about a week ago when I replaced my G27 wheel with a G29 (driving an SRV with a wheel is a blast, btw). This time I was able to replace every reference to to the device ID of the old wheel with the device ID of the new wheel and was back in business. Not exactly a straightforward process: it involved starting with a blank config and then mapping at least one button or axis, opening the new custom3.0.binds, extracting the ID and then pasting it into the old file in place of every instance of the old wheel. Without a backup I would have been lost here but the game backs up all your custom .binds files automatically now.
What mystifies me is why the game refuses to load the file at all if it can't find a particular device. With most games you'll find that everything still works except that device, leaving you with a lot less to sort out.