Justin--the Sirius Conductor is a special kind of device. I can't remember exactly how it works, but I believe that you need to do something along the following lines:
[NOTE: the following is meant only as helpful device. It may very well reset your device and could cause service interruptions by unlinking your remote and receiver, etc. Use at your own risk. :) ]
Receiver
1. Reset the receiver (press "remove device" in ThinkEssentials, press or press and hold the button on the side of the receiver-- can't remember which)
2. Add the receiver (press "add device" in ThinkEssentials, press or press and hold the button on the side of the receiver--can't remember which)
Remote
The remote is trickier. What you may need to do is figure out a way to link the receiver to a fully reset remote and then add in your ThinkStick or transfer primary role to your ThinkStick. The conductor remote/receiver seem to be designed somewhat as a standalone system which can use a Z-Wave device as a repeater--but that may just be my thinking from really old firmware that I used when it first came out. Nifty device though!
If the above steps don't work for you, please contact the manufacturer of your remote or refer to the Sirius Conductor manual for more assistance. Unfortunately, we can't provide technical support for 3rd-party products, but hopefully this is at least helpful...
Chris