I want to detect when a player would morph his two HTs into an Archon.
I am currently using Unit Groups to determine the number of units left for a player. But when a player morphs his HTs, it kind of kills the system because the HT units are not removed from the Unit Group, and the Archon isn't added into it.

How do?

You should be able to detect when the merge ability is used in the Event of the trigger.

But what if the player cancels before it happens?

Run another trigger, but change the ability effect to cancel. There are lots of different point in the ability that you can detect, and I'm pretty sure you can detect when a player cancels as well.

Do you need to know when an archon is created, when the player merges two templar, or when the two templar merge together?

Just detect that the morph ability is executed or the actor morphing starts...

Tinker with the event thing until you find one that works for the Archon merger.