EMB145 CREW ON ARR TO EWR HAS AUTOPLT DISCONNECT; WITHOUT AURAL WARNING; WHILE BOTH PLTS ARE BUSY WITH TFC AND FMS RWY CHANGES. DISCONNECT GOES UNDETECTED UNTIL TCAS TA AND A CALL FROM APCH.

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WE WERE TOLD TO EXPECT LNDG RWY 4R AT EWR AND NOT BEING REAL FAMILIAR WITH THE HONEYWELL FMS WE SET IT UP AND BRIEFED THE APCH BEFOREHAND. WE WERE GIVEN A DSCNT FROM 5000 FT TO 4000 FT AND TOLD OF TFC OFF TO OUR L AT 3000 FT THAT WOULD NOT BE A FACTOR. DURING THE DSCNT WE WERE TOLD TO HEAD DIRECT TO THE FAF FOR RWY 11 AND THAT THE TFC WAS STILL THERE. THE CAPT/PNF WAS LOOKING FOR THE TFC AS THEY SHOWED UP ON TCAS AS BLUE WHILE I/PF BEGAN SETTING UP THE APCH FOR RWY 11; THE AUTOPLT WAS ON AT THIS TIME. APCHING 4000 FT THE TFC ON TCAS TURNED YELLOW AND SAID THEY WERE CLBING INTO OUR ALT. SOMEWHERE IN HERE THE AUTOPLT WAS ACCIDENTALLY TURNED OFF; WITH NO AURAL 'AUTOPLT; AUTOPLT' SOUNDING. WE WERE BOTH TRYING TO FIND THE TFC TO AVOID AN RA AND THE NEXT THING WE HEAR IS ZNY TELLING US WE WERE 300 FT BELOW OUR ALT. WE NOTICED THE AUTOPLT WAS DISCONNECTED AND BEGAN A CLB BACK UP TO 4000 FT WHICH WAS THE ASSIGNED ALT. AT APPROX 3800 FT WE WERE TOLD AGAIN THAT WE WERE DEVIATING FROM OUR ASSIGNED ALT AND THE CAPT/PNF INFORMED THE CTLR THAT WE WERE AWARE OF THAT AND WE WERE CORRECTING AND WERE BUSY TRYING TO STAY AWAY FROM THE TA ON OUR TCAS. THE CTLR PROCEEDED TO TELL US AGAIN THAT HE NEEDED US AT 4000 FT AND BY THAT TIME WE WERE BACK AT THE ASSIGNED ALT. NEITHER ONE OF US KNEW HOW THE AUTOPLT WAS DISCONNECTED AS WE WOULD HAVE TAKEN IMMEDIATE CORRECTIVE ACTION HAD WE HEARD THE AURAL WARNING. THE TA COUPLED WITH TRYING TO LOAD AN UNFAMILIAR FMS MAY HAVE CAUSED SOME DIFFICULTIES IN SITUATIONAL AWARENESS THAT CAUSED US TO MISS THE ACFT CAPTURING THE 4000 FT ALT. A POSSIBLE FIX ON THIS PROB WOULD BE TO ENSURE EVERY ACFT ON THE 145 FLEET'S AURAL WARNINGS ARE WORKING PROPERLY AS SOME AUTOPLT DISCONNECTS AND TRIM WARNINGS DO NOT SOUND EVERY TIME. ANOTHER FIX WOULD BE TO ENSURE THAT CREWS FLYING AN UNFAMILIAR FMS IN HIGH TFC CONGESTION AREAS ARE FAMILIAR ON HOW TO ACCURATELY LOAD VARIOUS FUNCTIONS IN A BRISK MANNER SO THAT THEIR TIME MAY BE MORE CLOSELY SPENT ON MONITORING THE ACFT AND AUTOPLT. THIS CAN BE ACCOMPLISHED THROUGH BRIEF CLASSROOM SESSIONS DURING RECURRENT GND SCHOOL.