Hey, Cristopher! Thank you for the idea! I too encountered such a problem after reinstalling Windows. Thinking I got it all covered with a backup, but could only restore things like audio/graphics/etc, anything but not keybindings.
Just in case I've made a backup of original profsave_profile after fresh BF install and noticed something interesting: there were no keybinds, just GstRender, GstAudio and so on.
So it got me thinking that I need to change a couple of keybinds first - and I was right, after that all GstKeyBindings appeared, but I don't think it mattered.
Anyways, just like you said I've selected everything in my old file and replaced in the new created. For some reason fresh BF didn't like files that were created by "another" BF.
TLDR to apply your old settings from a backup if you reinstalled WIndows and/or BF2042:
1) do not simply replace PROFSAVE_profile! if you did, then you should probably delete it, launch BF2042 and it will generate a new default one;
2) open your backup PROFSAVE_profile (Notepad will do), select everything and copy it to the default one.