After Resetting a Skill Tree, Construct Specification, all equipped Construct Modules a were destroyed. They didn't return to Inventory.

Upon logging out and back in, previously destroyed Equipment Modules returned however the game still considered the slots to be empty. Also previously destroyed Weapon Modules returned however, if you changed them in any way before logging out after the reset the Weapon Modules are gone for good; think this would also be the case for Equipment Modules too.

So to summarize I could of lost a maximum of 25 Modules after resetting a skill tree.