Date: 201403
Local time of day: 1801-2400
Location: ZNY.ARTCC, NY
Light: Night
Aircraft: Heavy Transport; Low Wing; 4 Turbojet Eng
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Cruise
Airspace: Class A ZNY
ATC / advisory: Center ZNY
Reporter organization: Government
Reporter function: Enroute
Reporter qualification: Air Traffic Control Developmental
Human factors: Confusion
Second reporter function: Enroute
Anomaly: ATC Issue All Types; Conflict Airborne Conflict; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Result: Air Traffic Control Issued New Clearance; Air Traffic Control Provided Assistance
Contributing factors: Procedure
Primary problem: Procedure

Narrative: Aircraft X comes to the sector I am working from Sector 89. On the boundary is AMENO when the aircraft reports AMENO via HF radio he advises his next way point is 39n050w; which generates a message that advises me to verify his route of flight since that next point is not correct.  I then notice the flight had filed two flight plans.  The flight was flying the other flight plan which was filed before the current or most recent filed flight plan.  They were flying AMENO 39n050w 44n040w 47n030w 48n020w Bedra Nertu.  The flight profile in Atop that was being protected was not that it was AMENO 34n055w 39n050w 43n045w 47n040w 52n030w 56n020w Balix Ninex.  Once the flights routing was confirmed and reissued the flight was off course according to what Atop had projected for the planes position. Once the current lat and long was obtained it was clear that since this was caught early enough he was not very far off projected course.  The Sector 89 Controller received the same message as I did; when Aircraft X progressed BAROE; and said the flights ensuing was 39n050w this should have been enough to show the Controller that his route needed [to be] verified.  If that would have been completed than Aircraft X would never have been off course and unprotected.  Contact Aircraft X dispatch and advise them of the correct procedures when filing a new flight plan; this includes canceling the invalid flight plan.  Recurrent training on all the error messages and SYS messages that Atop generates. This is not the first time this has happened in the last two weeks; and it is almost identical situation to what happened to me last week.  The increase work load and the fact that the flight was not being correctly profiled could lead to a loss of separation.  These 'SYS' messages need to be addressed; and this is unacceptable.


Second narrative: I took coordination on Aircraft X from San Juan Center. When the plane came over BAROE; and estimated over AMENO; with his next point being a 50w coordinate. The system gave me a message saying points were given that weren't expected. I accidentally deleted this message. I took a break; but believe he may have lost lateral separation with another aircraft. I think it may have been a [specified] flight. I was told that the Aircraft X filed three flight plans and the wrong one was active. Routings may need to be verified better. Especially if there are multiple flight plans.


Synopsis: ZNY ARTCC Controllers state a flight had multiple flight plans and was using the one that the controllers were not using. This may have caused a loss of separation.