Comment 120 for bug 1431753

> Right, that usually doesn't happen when you upgrade to a new version of
> the same driver (for example upgrading nvidia-331 from 331.19 to
> 331.25). However, when you are migrated to a different driver package,
> e.g. from nvidia-331 to nvidia-340, you will lose your settings, because
> they are different packages and they provide different alternatives

Yes, I know. But since in this case installing a different driver packages was forced by an update (without even a warning or asking for confirmation, btw), whatever process was responsible for that should take that into account and take care of "migrating" the settings.

> This, while unfortunate, is not a bug,

Yes it is. You are only giving a diagnosis of the exact cause of the bug (which by the way I already knew), but that doesn't make it less of a bug.

> and we cannot change it, due to
> the way alternatives work.

I seriously doubt that's IMPOSSIBLE to fix. It may not be easy, but if you can do it manually, it can be done automatically. You only need to produce a script that looks at the settings (alternatives, or whatever) before uninstalling the old package, and then applies them (with all the necessary remappings and modifications) after installing the new one.
It may be a lot of work but it's NECESSARY and it was part of fixing this issue. A part that hasn't been done.