ZTL Controller reported a clearance issuance based on the pilot's cancelled clearance which led to a CFTT and an airspace violation.

Narrative

Aircraft X called; on the ground at JZP airport; looking to pick up his IFR clearance. The D-side next to me was in training so I let them pull up the flight plan for me. The flight plan they pulled up for me was JZP...ZZZ...ZZZ1...ZZZ2... I cleared the aircraft from the JZP Airport to the JZP Airport as filed and since the first fix on his flight plan had him making a turn out to the NW after Departure; he was released.Shortly after; Aircraft X called up; departing JZP and heading SE bound. At the time it was not a factor with anything; he was radar identified and I waited for him to make his turn to the NW. Once the aircraft was about halfway between the JZP Airport and Atlanta approaches airspace; I told the trainee and trainer to 'watch this guy with A80 because he still isn't making his turn.' Immediately after this; the trainee got sidetracked with trying to get a point out on a guy climbing off of ZZZ1 which did not need our attention at that moment. Realizing this; I quickly called the NE side of Atlanta approach to start pointing out Aircraft X. Unfortunately; our MIA (Minimum IFR Altitude) in that area is 041 and the aircraft was at 038 so there wasn't anything I could do at this point. The NE side approves the point out; the trainee gets on the line with the NW side of Atlanta approach to start making the point out. While they are on the line; I ask Aircraft X when he is going to make his turn to ZZZ. The aircraft responded; 'I'm heading to ZZZ3.' As I'm questioning the aircraft; he starts flashing CA (Conflict Alert) with an aircraft at 050 in A80's airspace. I do the only thing I can do. I stop him at my lowest altitude of 041 and turn him to a NW bound heading immediately upon reaching to keep him away from A80's traffic. According to the D-side; A80 was watching Aircraft X and they said they would keep him separated. This took both me and A80 having to issue extreme headings to our aircraft and the situation should have never got to that point.After getting the aircraft safely away from traffic and away from A80's airspace; we figure out that the pilot had originally filed the flight plan I issued him but removed it and filed a different flight plan going to ZZZ3. When the D-Side pulled up his information; they had the info on the flight plan that we issued him (going to ZZZ) but not the info on the new flight plan going to ZZZ3. Since we were unaware their were 2 flighplans; I issued him a clearance 'as filed' assuming he would depart JZP to ZZZ and not ZZZ3. The aircraft assumed his old flight plan was removed and he was given a clearance to depart and go to ZZZ3. This is what led to the aircraft getting to close to A80's airspace and the lack of timely information exchange/point outs led to A80 having to vector out their aircraft for Aircraft X.Knowing there was 2 flight plans on file would have alleviated this situation