That would make sense then since the emunand partition is where the info on installed games is stored. Unless you were able to copy that partition to the new SD card you would need to reinstall the games. Just like if you were to boot OFW, but your games were installed in emunand. They would show up as archived and would want you to download them again.
I would make sure you have your saves backed up and just try reinstalling. Would be better to delete them first in my opinion and then install again, but just reinstalling might work as well.
I personally use SD files since at this time it's easier to migrate to a new SD card since you can easily access all the needed files. I believe at some point there will be a utility or option for backing up the hidden partition though and I am sure there are ways through a computer, but might not be simple.
