That's one nice thing about the LPE200 that davidbond21 made me purchase- it will automatically scan for the correct CC (assuming you've programmed it in there) once the CC has been changed.
Scanners are no different. You don't set where the control channel is in the LCN lineup; you simply enter all the frequencies in the radio and scanner, and both just scan all the channels until it finds the CC, at which point it gets to work trunking.
The control channel might be changing LCNs, but the frequencies are largely set in stone. You can even put all the frequencies in completely wrong LCN slots, and the radio and scanner will still pick up the control channel(because it scans all the channels automatically to find a CC) and go to work trunking, though it will be completely screwed up and will not follow the conversations correctly, if at all. Example: Say you swapped the frequencies in LCN 1 and LCN 10. Basically, when the control channel sends out info that a group call is being made on LCN 1, your radio/scanner tunes to the frequency in slot 1. Except in our example this is actually the frequency of LCN 10, which means that if there is no activity on the proper LCN 10 at the time the scanner/radio will be silent; or if that voice channel is being used by another talkgroup at the time, you'll hear that traffic.
Don't get hung up on the CC position because this is virtual and can change as many times as needed. The concern needs to be 1)finding the frequencies used and 2)finding the correct LCN order of these frequencies. CC finding and following is done automatically on both public safety radios and consumer grade scanners. Put all the frequencies in the correct order and the equipment does the rest.