Really guys, who cares if you changed out your mods and don't get "free upgrades." You'll be upgrading this gear in weeks, if not days. Plus, at this point story mode drops Rakata, so you could always run that to replace the gear. Doing HM and dailies will help you upgrade the rest. I know it's not min-maxy, and it sucks that we're being "punished" for trying to optimize our stats, but you don't have to live with it forever.
You also have a few more weeks of raiding to replace whatever gear you modded, so really, it's no biggy.