do you have access to a terminal?
if so navigate to ~/.local/share/mupen64plus/save/
$ cd ~.local/share/mupen64plus/save/
then enter ls to get a list of files in that directory
$ ls
you should see 2 savegames for every you have played before and after the update.
the old savegames filename should be mostly in capitals, for example:
THE LEGEND OF ZELDA (unknown rom).sra
and the new savegame filename should be someting like that:
Legend of Zelda, The - Ocarina of Time (E) (M3) (V1.0) [!].sra
now you need to copy the old savegame over the new one, for example:
$ cp THE\ LEGEND\ OF\ ZELDA\ \(unknown\ rom\).sra Legend\ of\ Zelda,\ The\ -\ Ocarina\ of\ Time\ \(E\)\ \(M3\)\ \(V1.0\)\ \[!\].sra

and you should have your savegame back. adjust the above line to your needs, i just used common rom filenames