So I purchased my first set of Adaptive armor from the cartel market (free points are free points after all) , and transferred all of the mods from my old Rakata gear, to include armoring, modifications, and enhancements, and the set bonuses did not go with the armoring mods, which is how I understood the process to work. Is the older PvE gear not compatible like this, or is there some sort of ceremony that I have to partake in to get the bonuses where I need them?

In Rak, Colum and Tio the set bonus is in the shell, so no the bonus doesnt transfer on this.

I'm not up to that gear, but people seem to ask this a bit... aparently the set bonuses on cirtain sets are attached to the shell of the gear, not the mods

 

[Edit]: looks like I was beaten to it ^^

Edited December 20, 2012 by Ithilwen

Set Bonuses of Battlemaster, Tionese, Columni and Rakata gear are bound to the shell.

Only (Elite) War Hero, Campaign, Dread Guard and Hazmat gear's setbonus is bound to the armoring.

Edited December 20, 2012 by Creror

Battlemaster, Columi, Rakata -> Set bonus is on the gear shell

 

Champaign, Dreadguard, Warhero, Elite warhero -> Set bonus is on the armoring

All you have to do is replace the Rakata Armoring Mods with the Campaign ones, which you can buy from the Supply Black Hole/Campaign Vendor on the fleet and you'll get your set bonus back. Plus the Armoring Mod is more powerful then the Rakata one so you'll increase your stats.

 

You can buy the Campaign Armoring Mods with Black Hole Com's.

Edited December 20, 2012 by Monoth

All you have to do is replace the Rakata Armoring Mods with the Campaign ones, which you can buy from the Supply Black Hole/Campaign Vendor on the fleet and you'll get your set bonus back. Plus the Armoring Mod is more powerful then the Rakata one so you'll increase your stats.

 

You can buy the Campaign Armoring Mods with Black Hole Com's.

 

Yep. Do this. They made them reasonably cheap to make up for this.

Awesome, thank you everyone!