Phantom storage after transferring to a new SD card

[iceedge]

TL;DR - I transferred all my files and the EmuMMC partition from my old SD card to my new one. When I loaded my new SD card all the games were telling me I had to redownload them. I ended up reinstalling through Tinfoil but after reinstalling I noticed my storage dropped by a lot (I have a 512 GB card). I'm guessing instead of overwriting the files, it's duplicated now. Is there a way to clean up the old files from the original NSPs?

Added context:

I was transferring from SXOS to Atmosphere, which I had a hard time for a while, which might have been made worse by the fact my SD card ended up being corrupted in the process. I might have some garbage files in there and corrupted files mixed in.

 

[iceedge]

Also, I noticed that I have both an Emutendo folder as well as an emuMMC folder. I'm wondering if this is the reason why? And which one should I keep?

 

[SonyUSA]

Sounds like you didn't generate the Nintendo hashed folder first then copy your old folders into that. Also, just rename one of the boot0 files in the emummc/emutendo and see which stops it from booting, then you know which one you're using.