Without knowing your control or machine, I would suggest that there is probably a zero offset adjustment parameter somewhere in the control.
Normally the value is associated with the number of steps of the drive motor.
Once you find the proper parameter, you would need to adjust the value to get the A axis "level".
Another possibility comes to mind....
Some rotary axis devices have a physical switch or sensor to tell the control where "home" is.
It is possible the switch or sensor got moved during the rebuild and not put back in the same place.
ObrienDave. MasterCam since V6. Gcode since 1983.
The nose you punch today may belong to the butt you have to kiss tomorrow.