So to retrace my steps, I downloaded reHID because I thought it may be useful in the future, enabled it, realised it made ZL and ZR not work in games (still works in home menu), deleted the application (installed cia (which did nothing because thats not how it works)), found rehid.cxi then...
So, I transferred my save files from Citra (to continue my gameplay on 3DS) into the 3ds/Checkpoint/saves/0x01BFB Metroid Samus Returns folder, and the folder containing the save files (MSR has multiple for different things) is under the name profile0.
Now, I used checkpoint to restore these...
I may try the new ram site, and download more RAM to my Switch. Not sure if ddr3 is the right ram
for it tho. Edit- no it uses floppy Ram, just like @AncientBoi