A FALCON 20 IN CRUISE AT FL330 NOTED SLIGHT YAW. ON START OF DSCNT NOTED YAW IN OPPOSITE DIRECTION. ON LNDG FOUND #1 ENG LOWER COWLING OPEN AND #2 ENG LOWER COWLING MISSING.

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I ARRIVED AT THE ARPT AT XA:30 DEC/WED/02. I WENT TO THE ACFT TO DO A PREFLT INSPECTION. IT HAD SNOWED ALL DAY AND THERE WAS ABOUT 2 IN OF SNOW ON THE ACFT. SINCE I WAS SUBSTITUTING FOR THE NORMAL FO AND NOT BEING FAMILIAR WITH NORMAL PROCS ON THIS SCHEDULE RUN I ASKED THE MECH WHAT THE NORMAL PROCS WERE. HE INFORMED ME THAT NORMAL PROTOCOL WAS TO LEAVE THE ENG PLUGS IN SO THE ENGS COULD BE PREHEATED. NORMALLY; I WOULD TAKE THE PLUGS OUT; PITOT COVERS OFF; CHECK THE GAS CAPS; CHECK THE OIL; ETC; AND DO A NORMAL PREFLT. THE MECH INFORMED ME THAT HE HAD ADDED 2 PINTS IN THE #2 ENGS AND 1 PINT IN THE #1 ENG; SO I DID NOT CHK THE OIL. I DID A PREFLT AND 'LOOKED' AT THE COWL LATCHES NOTICED THAT THEY WERE CLOSED. THE MECH INFORMED ME THAT HE WOULD PRE-HEAT THE ENG AND I WOULD UNLOAD THE 1ST TRUCK AND THEN DO COCKPIT SET UP WHILE THE CAPT UNLOADED THE 2ND TRUCK; SO THAT'S WHAT I DID. THE MECH FINISHED THE OUTSIDE PREFLT AND REMOVED THE PLUGS AND PITOT COVERS. WE THEN STARTED THE ENG AND TAXIED TO THE DEICING EQUIP TO DEICE THE AIRPLANE. WE DEPARTED AROUND XB:30 LOCAL ON RWY 13 AND CLBED AND FL330. CRUISING AT FL330 ON AUTOPLT WE DID PAPERWORK. ABOUT 1/2 TO DESTINATION WE HEARD THUMP AND THE ACFT YAWED TO THE R. THE CAPT TOOK CONTROL WHILE WE ASSESSED THE SIT. THE AIRPLANE FLEW FINE AND ENG PARAMETERS WERE GOOD. WE CONCLUDE THE CTL SURFACE OR CONNECTION HAD A BUILDUP OF ICE AND BROKE LOOSE SO WE CONTINUED FLT. UPON DSCNT INTO ARPT WE HEAR ANOTHER THUMP AND THE ACFT YAWED TO THE L. AGAIN ENG INSTRUMENTS INDICATED GOOD AND WE DID A NORMAL APCH AND LNDG. ARRIVING AT THE RAMP WE INSPECTED THE ACFT AND FOUND THE #1 ENG LOWER AND INBOARD COWLING AJAR; AND THE #2 LOWER OUTBOARD COWLING MISSING. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: THE RPTR STATED WHEN INVESTIGATING THE CAUSE OF THE DAMAGED #1 ENG LOWER COWLING AND THE LOSS OF THE #2 ENG LOWER COWLING IT WAS DISCOVERED THAT THE LOWER COWLING MUST BE CLOSED AND LATCHED IN A PRECISE SEQUENCE. THE RPTR SAID THE LOWER COWLING HAS THREE LATCHES AND THE CENTER LATCH MUST BE CLOSED FIRST SINCE IT HAS A CENTERING PIN THAT ALIGNS ALL THE LATCHES. THE RPTR STATED CLOSING THE COWLING IN ANY OTHER SEQUENCE WILL NOT ALLOW POSITIVE LOCKING EVEN THOUGH THE LATCHES APPEAR LOCKED.