Sorry, but it sounds like you're missing a few important facts...

• A 'Magic Memory Stick' can be used for Pandora and to store games/emulators at the same time - that's what my blue SanDisk one is doing at the moment.
• If you use the UMPS installer, you can not only do everything from the PSP, you can also use a Pandora battery as a regular one.
• I can't think of any reason why you'd want to copy the folders over by hand in the first place.

So basically... you can make your battery a Pandora, your MS a Magic MS, and just leave them like that, while still using your Magic MS to store games, etc, and using your Pandora as a regular one.

(The UMPS installer installs a different IPL to the normal one, one which only boots into the Pandora menu if you hold L while starting the PSP. This Pandora manu gives you access to Despertar Cementario v3, the original Pandora menu, and some files and ulilities. I'll write a tutorial... if/when I can be bothered.)

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