By reinstall you mean… deleting the program’s archives and re-downloading it? (Sorry for the dumb question)
And if you do, will that delete my progress in my games?
Sorry for being such a pain in the backside.
Move everything inside C:\Users\%username%\AppData\Roaming\Citra\ to another folder.
redump your system archives(nand folder), and copy it to C:\Users\%username%\AppData\Roaming\Citra\. also redump your roms.
All of your save files are located on the folders extdata and title on: C:\Users\%username%\AppData\Roaming\Citra\sdmc\Nintendo 3DS\00000000000000000000000000000000\00000000000000000000000000000000
so, just backup these two folder to keep your save game data.