Is there any convenient way to migrate the MC43 code to MC43FS module?

To change from one type of master module to another, first add the new module (E.g MC43FS) to the system layout. 

In the application view of the original master, Ctrl-A to mark all function groups and channels and drag and drop to the application of the new master. All at once. 

On the block diagram of the original master, do the same. Ctrl-A to mark all channels, drag and drop over to the new master. 

In the system layout, drag and drop all buses over to the new module.

If you have event- or statistics logs, drag and drop these over to the logs node for the new master.

Measure groups, Adjust groups and Security levels are project wide and requires no action. 

Check that you have the same properties on the application cycle time.

Check that you have the same properties on the module (CAN termination, J1939 properties)

Check that you have the same properties on module pins (PWM frequencies and open load detection)

Now you can delete the old master.