Yes, this is noted in the datasheet (for command A0/A1):
This command only affects subsequent data input. Data already stored in GDDRAM will have no changes.
As is the fact that a vertical flip takes effect immediately (for command C0/C8):
Additionally, the display will show once this command is issued. For example, if this command is sent during normal display then the graphic display will be vertically flipped immediately.
I should probably add these facts to the Arduboy2 library documentation.