Why would changing fluid cause rough shifting?
Because the transmission adapts to the old fluid as the fluid wears. New fluid is a change in viscosity and friction characteristics.
A lot happens in a shift, the throttle is closed (pedal position doesn’t matter, only throttle body valve position, which is computer controlled), a solenoid is opened, releasing fluid from one gear, the torque converter clutch may, or may not be released, and a solenoid is closed, driving fluid into the servo for another gear.
The computer monitors those operations, and if the timing isn’t right, if the shift isn’t smooth, adapts the timing to make them smooth. It takes thousands of shifts to adapt unless the adaptations are reset.
A new valve body, for example, requires a “relearn” of all of that and the first few shifts will be rough. There is a very detailed procedure to go through an initial adaptation for garage shifts (R-N-D) and each gear shift up and down. The car must be placed in adapt mode by VIDA. I’ve done three valve bodies.
That said, the degree of adaptation depends on the degree of wear of the old fluid. If it’s bad, then, yeah, it’s a big change and the transmission won’t shift right.
The quick relearn is required for component replacement. It may be required for fluid replacement.
I think
@YZJB gave you good advice. When I do a flush, I reset the counter using VIDA. I flush often enough that I haven’t had to reset the adaptation because the fluid is in good shape, but I have the AW-55, which is a simpler five speed than your six speed. I would listen to the guy who has several cars like yours.