Greetings Deg,
If I understand you, I have just had the same problem. Your problem is that with the cycle waypoint he no longer waits for your commands, correct?
Well, two things.
1. Make sure the Radio triggers are set to "Repeated". If they are not, they will disappear from the list after being called once.
2. Importantly, set the Radio Trigger type to "Switch". It should be a little drop-down box which, IIRC, is blank to start with.
So for example, you Heli lands and waits for Radio Alpha to go. He then moves to the LZ where you use Radio Bravo to tell him to go back. Place a move waypoint and then a cycle near the original base. Make sure both Radio Triggers are set to "Switch". This way they will interrupt the cycle, and force him to wait for your commands.
In addition, you can set a trigger run by "BLUFOR PRESENT" at a spot and set it to repeated, so that he doesn't run out of fuel. Example, place one at the base and put in On Act.: helicoptername setfuel 1. (Helicoptername is the name of the heli, and 1 is a full tank of fuel. Use 0.5 for example for 50% fuel).
Hope that helps. If you need more help with this just say (preferably a PM) and I can make a document or a movie.
Greglo. :)