You can't just backup the folders with the eboots and expect to be able to transfer them back. When the guide says to backup VitaShell/MolecularShell, it means using CMA to do this. If you don't have a PC, then you're kind of out of luck there.
You'll have to change back to the other memory card if you want to use them again. I suggest moving at least the Molecular Shell install to ur0 using Application Storage Manager, so you still have access to Molecular Shell when swapping memory cards.