I don’t think Regina instructed Jefferson to release Belle. Jefferson is acting against Regina now. I don’t think it’s just a rouse that the writers are trying to pull. There is real and existing animosity between Regina and Jefferson for the time she left him stranded in Wonderland and for the time she refused to reunite him with Grace.
I think it’s likely that he knew about Belle from something that happened which the audience hasn’t seen yet. Jefferson is insane (aka the Mad Hatter). Perhaps Jefferson came back from Wonderland and was held captive in the same jail as Belle in FTL. The other more likely scenerio is that Jefferson was kept in the hospital basement when he first came to SB before Regina put him under house arrest for 28 years. That would explain how Jefferson knows about Belle.
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy