Board Thread:Spoilers!/@comment-26196542-20150930211355/@comment-24674051-20151013160721

As for merlin being 'Free" when he gave Emma the warning, I'm not sure.  Because the Apprentice was talking to Merlin via Blue Smoke right after the Emma/DragonEgg incident, which would be around 8 years prior to Merlin's warning to Emma.

My guess is that Merlin has been trapped for a while, but can still communicate with the outside world. In Emma's case, we have no proof that the whole conversation did not take place in her head, and we know that even back then that Emma had strong potential for Magic, which might have allowed for a brief contact between Merlin and Emma.