ACR X ON TKOF ROLL HAD LTSS WITH ACR Y XING RWY. ACR X EVASIVE ACTION TAKEN ABORTED TKOF. SYS ERROR.

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JFK ARPT WAS HARD IFR AS INDICATED ABOVE. WE WERE USING THE ILS RWY 22L APCH AND DEPARTING RWY 22R. WE WERE UNABLE TO SEE EVEN THE TAXIWAYS SO EVERYTHING WAS BEING DONE BY PLT RPTS AND ASDE. THERE WERE 2 LCL CTLRS; ONE FOR TFC ON THE APCH; AND ONE WAS WORKING THE DEPS OFF RWY 22R. ALL OF THE ARRS EVENTUALLY HAD TO CROSS RWY 22R TO GET TO THE TERMINALS. THE ARR LCL WAS HOLDING THEM SHORT AND INDICATING WHICH INTXN THROUGH STRIP PLACEMENT AND MARKING. AS MY TFC PERMITTED; I WOULD AUTHORIZE THE ARR LCL TO CROSS; WHEN APPROPRIATE; ALSO STATING WHICH INTXN AND/OR HOW MANY. THE ARR LCL ACKNOWLEDGED THIS COORD EACH TIME; AND ADVISED WHEN CLR. I CLRED ACR X FOR TKOF AND PUT ACR Z IN POS ON THE RWY. I TOLD ACR Z IT WOULD BE 'A MOMENT OR 2 IN POS FOR IN TRAIL RESTRICTIONS.' THE ARR LCL QUESTIONED MY INTENTIONS WITH ACR Z. O I EXPLAINED THAT I WAS GOING TO HOLD HIM FOR SPACING BEHIND A PREVIOUS DEP AND TO ALLOW HER TO GET SOME OF HER TFC ACROSS. (I DID NOT STATE 'CROSS RWY 22R' NOR DID SHE ACKNOWLEDGE A XING). A MIN LATER; ACR X ADVISED THAT HE ABORTED HIS TKOF BECAUSE AN ACR Y HAD CROSSED THE RWY. APPARENTLY; THE ARR LCL HAD MISTAKEN MY ANSWER TO HER QUESTION TO BE COORD; AND HAD CLRED ACR Y TO CROSS RWY 22R. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: THE RPTR STATED THE ARR LCL CTLR HAD CLRED 3 ACFT TO CROSS RWY 22R IN FRONT OF ACR X ON TKOF ROLL. ACR Y; LGT; HAD BEEN CLRED FIRST AT TAXIWAY F. ACR X HAD JUST STARTED TKOF ROLL; SAW ACR Y; AND ABORTED DEP. CLOSEST PROX WAS 1000 FT. BOTH LCL CTLRS WERE DECERTIFIED. ASDE RADAR WAS GIVING A GOOD PRESENTATION OF ACFT ON THE RWYS.