TLDR; Hold both the On button and the scene 1 button on the remote while near the bridge performs some kind of reset that isnt the same as a hard reset.
I have had a set of Hue lights since I was givent them while at Braintree's Battlehack last year. When I first set them up I used the hue bridge but shortly bought a second hand living colors remote. I completely disconnected the hub and packed it away.
Then amazon put a load of the living color Blooms and Aura's on sale, and I bought myself some new toys.
I dragged out the bridge and quickly found that I just couldnt get the remote to transfer the lights via touchlink.
A quick search of the forums brings up plenty of suggestions and solutions, however as it typical none of them helped at all. The most common being to telnet into the bridge on port 30000. When I tried this the bridge refused the connection.
After almost giving up I stumbled across a button combination not listed in the remotes manual... If you put the remote near the bridge and hold BOTH the on button and the scene 1 button the bridge will preform some kind of reset (Possibly channel?), once it restarts I found I was able to perform a normal touchlink connection.
Hopefully this information helps someone else!