Unfortunately no they do not come with you. and I don't know why they changed it.

i liked that feature in the old client!

I bet I know why.

I just figured out today that you can train and house more than a squads worth of units in your colony directly. I don't know how high the limit is for that, if there is one at all but I bet they don't come with you when you relocate to prevent players from simply putting ALL their units inside their base b4 relocating....

That's Willow's theory anyway >>

Yes that would make sense. But they could give the ability, just limit it to 1 or 2 squads.

As it is now, the main base does take on the properties of a squad. Try placing units into the main base. At some point it'll say the squad is full.

I have 10 tanks building right now (= 30pts), and I can't even transfer 1 infantry unit back into main base. But I can still build more units.