is there a way using triggers totransform a creep colony into a sunken colony?

You can remove the creep colony and create a sunken colony on that position.
(center location, remove creep colony, create sunken colony)

Maybe some ai script will cause that a creep colony sometimes morphs to a sunken near important buildings inside the base.

I can't create a sunken colony because creep colonies are on unbuildable terrain

Well you could place a neutral sunken underneath the creep colony, then remove the creep colony and give the sunken to the designated player.

Stack 2 creep colonies, then remove one and you can create the sunken. Then remove the last creep colony.

Yeah I was playing one of FaRTy's SunkNess Defense games and it featured a 51 stacked Zerg Creep Colony structure. He explained to me that when you have a building created and then you remove it, the designated space underneath the unit to which was just remove, gets placed as buildable terrain. Then you go from there creating a Zerg Creep Colony, remove it place the Zerg Sunken Colony, then remove one of the Neutral Creep Colonies. I'm pretty sure that this is the correct order.

Couldn't you just create the sunken elsewhere on the map where buildable terrain is accessible and the use the move trigger to swap it in with the creep? I'm not sure if buildings can move to unplaceable terrain like that though, but it's worth a try. Unless you're on the instillation tileset.

The method mentioned works fine. The only downside is that you have to have a previously stacked unit there and removed for it to be considered buildable terrain for the player to build a creep colony on.

50*, and that isn't what it was called.
And it wont make already unbuildable terrain buildable, only buildable terrain that has had buildings.