[Alonzoortiz87]

I have been trying to set up a station using a 6-axis Fanuc robot synchronized with a 2-axis turntable. However, there seems to be a problem with the robot base moving to the 2-axis turn table when synchronizing. I would like to keep the robot base on the default Fanuc 6-axis robot base frame. To demonstrate the problem, here is a picture of the set up when the 6-axis robot is not yet synchronized to the 2-axis turn table. I have set a reference frame positioned at (2000.000, 0.000, 1040.000,  0.000,  0.000,  0.000). 
   

Then after synchronizing the robot to the 2-axis turn table, the robot base automatically moves to the turn table base. You can see in the following picture how the reference frame automatically changes to (2000.000, -1000.000, 970.500, 0.000, 0.000, 0.000). The actual location of the reference frame is in the same place, it is only now referencing a different robot base location. 
   

The issue is then further complicated because the tool frame (6-axis robot flange) is now tied to the 2-axis turntable. So any movement of the turn table will also move the tool frame with respect to the reference frame. When generating a robot program, this causes the coordinates to move with any turn table movements.  
     

Is there a way to modify the robot base location so that it can be placed back on the 6-axis robot arm and also not be tied to any axis?

[Sergei]

When synchronizing the positioner in RoboDK, the external axes are synchronized with the robot and start working in the so-called cooperative (coordinated) mode. This is why the base transfer you described occurs.

Working in the cooperative mode allows you to move the tool at a given speed relative to the trajectory when all axes are used.

As far as I understand, you want to work with external axes that are just synchronized (non-cooperated).
Since RoboDK works with external robot axes only in cooperative mode, you can try to enable cooperation with external axes on the robot controller (this is supported by most manufacturers).

Alternatively, you can modify the postprocessor to output the coordinates of the tool relative to the robot base and the values of the external axes separately.