Yes, they are dating when the show went off the air. They broke up when they were told to but they couldn't stay apart. Jules was dating someone else but then she realizes he wasn't the man for her. In season 4 episode 1 Jules comes to Sam's apartment and they get back together until Sam's sister walks through the door. In the end of the episode they get back and ever since that they went against the rules and got back together. Greg finds out about them and keeps the secret but soon they were caught when Sam's and Jules conversation was recorded. The chief of the SRU allowed them to stay on the team and stay together as long as they could stay focused and be able to put citizens first.
Sorry this was kinda long because it was just a simple answer but i know so much of flashpoint that i can babble all about it. Also sorry if my spelling or punctuation is messed up i suck at that kind of stuff.
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