How to homing the A-axis again with gcode?

There is no way to 'unhome/rehome' a joint in gcode.
There is a modified 'orient' component that allows optional rehoming to an encoder index signal before doing the spindle orientation.
This post contains a config for spindle/rotary switching in gcode using the modified 'orient' component to rehome the spindle before switching to rotary mode. (This requires an encoder with index on the spindle)
forum.linuxcnc.org/38-general-linuxcnc-q...blem?start=20#324276

I can think of a few ways that you might be able to "reset" the A axis, but I don't know if any would work properly.

Firstly, you can't run the actual homing sequence in "Auto" mode. That's a pretty fundamental limitation that prevents homing while a G-code program is running.
If you don't need that (though I think that you probably do) then there are ways such as G-code remaps or custom-Mcodes that could do that.

You could try using the G10 command to reset the A-axis position, though.
Asuming that the A axis is calibrated in degrees:Will "unwrap" all the full-turns that have happened in spidle mode.
However you need to keep in mind that all the full turns are still there, and at some point there will be enough full turns that you will lose precision in the partial turns. The spindle position is a double-precision float, with about 14 significant digits, so this will take some time but you would probably still want to re-home the A axis manually between every few dozen jobs.

I can't immediately think of a way to do what you ask.
It would be possible if M5 was re-mappable, but I don't think it is.
If you can use (for example) M15 in place of M5, then that could be remapped to:
wait for spindle stopped
measure the current angle
reset the offset (as described earlier)
rapid to A=0

linuxcnc.org/docs/stable/html/remap/rema...remap:existing-codes