@Lolonois: Thanks. I have already updated my Pi3b and Pi400 using the official released Retropie version from Midwan. I also compiled myself releases since around Christmas 2021 and reported all bugs I found on my old Pi3b to Midwan, which were all fixed up to the v5 stable release.
@nemo93: Update process was quite smooth. Just compile or copy official zip package and copying over some files to the right Retropie spots and you are good to go. As I switched around last Christmas from ADF to WHDLoad, I can‘t report much on .uae files, as I do have no real need for them anymore . For compatibility I created an A1200 profile and saved that as default.uae.
For WHDLoad games I recommend setting up Port 0+1 with two game controller and enable the mouse/joystick auto switch feature under Input to switch mouse and Joystick by simply pressing left mouse or fire button. This allows to play Bubble Bobble or Blood Money with two Joysticks and still enable trainer etc. by simply clicking LMB on WHDLoad workbench screen and fire button once game is loaded.
In addition I would recommend to set whdload_quit_on_exit=truein .uae files, respective set default_whd_quit_on_exit=yesin amiberry.conf. This forces WHDLoad games to call AmiQuit when quit WHDLoad games via F10. Without this option, user may get trapped in the AmigaDOS prompt, from where you could enter AmiQuit + ENTER manually to go back to ES menu.