Hi,
of course the MEGA65 will be updated continousely. our vision is, since it's open-source, that it will be updated not only from us, but from the whole community.
We expect, that once the MEGA65 is released, that people will start to port cores over to the MEGA or add features they would like to have, like i.e. Userport, Datasette port...who knows....
At the moment the update is done via a programmer on the MEGA65 pcb and via SD card on the Nexys4 board.
We plan to change the way how to update in the future...
I hope this answers your question ?