Although the whole reason I jumped to using rsync is that Windows was spitting some weird errors when transferring the games on it.
Turns out the two microSD to USB adapters I had are identical as far as the kernel is concerned and they sometimes drop out or disappear mid transfer.
I just hope I haven't corrupted anything, lmao.
Update: the original SD card is either corrupted or the readers are Just Fucking Shitty.
It did the thing of dying mid-transfer even when only reading from it, and now copying to a native SD card slot on another laptop I had.
So I now have to use either the adapter that came with my DS R4 (which is surprisingly reliable!) or my cool USB-C 3.0 hub thingy.
The worst part is that the hub's controller seems to be horrid.