I know this is an old post but did this ever get resolved? I've been having this issue for a while and I am still having it. It will read and play the games just fine but it never saves the correct path files for the cheats or covers.
Replying for anyone else. I use Jgecko u to export the cheat. Just choose which drive. Then using TCPGecko the latest one I click on X to use cheat engine and SD. I start up TPHD and it works as long as your cheat is good.
I use TCPGecko and it works fine. I open the homebrew channel like normal through the mii channel. Then I open the latest TCPGecko and JGecko U and choose A. If I'm using the sd cheats I choose X which enables the sd portion. I am on tiramisu forgot to mention that.