If someone want to change/install a custom theme without losing menuhax, follow these steps:
-Put the new theme on the menuhax folder.
-Run themehax manager (you can use the menuhax itself).
-Select the second option (the one that says "delete menuhax,clear the normal theme-cache...").
-Without exiting, select the first option (the one you use to install menuhax normally).
-Now, reboot your 3ds, go to home menu manager, and enter on "Change theme"
but you do not have to change the theme
(screenshot by
@Argentlan )
-Wait until the writting files to the sd had finished and exit.
-Reboot your 3ds pressing L or the button assigned to run the hax
-Run menuhax manager again and this time, select the 5th option ("install custom theme...")
And you're done.
I don't know if there is an easier way.