I've been porting my old A4 game to A5. The new API is pretty nice, with more consistent and easier to remember names and parameter orders than the old one (maybe except for al_key_down, hehe).
I don't know much about how hardware accelerated rendering works, so here goes. My A4 game used double buffering, and updates only the changed parts of the buffer, before blitting the whole thing to the screen.
For A5, I just removed the old backbuffer and draw to the default target instead, then call al_flip_display. This worked in windowed mode (Direct3D), but in fullscreen mode it seems to be using page flipping. At least it's doing something that breaks my partial updating scheme. Which in hindsight is obvious that I would have to expect.
Should I just update the whole screen every frame? I suppose I could use a video bitmap for double buffering and keep the partial updating system, but that seems a bit pointless.