I recently tried to craft a piece of set armor. This apparently changes its properties so that it is no longer a set item in terms of having all items in a set.

NEVER DO THIS!!! Your prized item will be trashed and look no better (or worse) than before.

I'll have to look at Bioware's script and customize it to save all the necessary information to the crafted item. Until then, don't craft unless you plan on ruining the set properties.