CTLR CLEARED THE WRONG ACFT FROM THE HOLDING PATTERN FIRST AND DURING THE DESCENT HAD LESS THAN STANDARD SEPARATION WITH AN MLG AT A LOWER ALT IN THE PATTERN.

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AT XA02 Z; MLG X CHKED IN AT 13000'. I WAS AWARE OF OTHER ACFT IN HOLDING BECAUSE I HAD TWO STRIPS IN THE HOLDING BAY; BUT I THOUGHT MLG X WAS MY LOWEST ACFT AT 13000'. THE OTHER STRIP IN MY BAY WAS MARKED 140 AND I THOUGHT THAT WAS MLG Y. AT XAO4 Z; I CLRED MLG X DIRECT TO MMJ AND DSNDED TO 9000'; THINKING HE WAS NUMBER ONE AND THEREFORE THE LOWEST. AT THIS TIME MLG Y WAS IN A 'CST' STATUS ON THE SCOPE AND I SAW HIM OUTBND THINKING HE WAS THE ACFT AT 14000'. ABOUT 30 SECONDS LATER; MLG Y ASKED WHERE HIS SEQUENCE WAS BUT DIDN'T SAY AN ALT; AGAIN HE WAS IN A 'CST' STATUS AND I ADVISED HIM THAT I WOULD HAVE LOWER SOON; THINKING HE WAS AT 14000' AND I WAS WAITING FOR MLG X TO BE CLR OF HIM. MY INTENTION WAS TO HAVE HIM FOLLOW MLG X. I NOTICED MLG X WAS INBND AND I TOLD MLG Y TO TURN INBND DIRECT TO MMJ; THINKING AGAIN THAT HE WAS AT 14000'; AND I WANTED HIM TO FOLLOW MLG X. MLG Y WAS TURNING INBND WHEN HE RPTED THAT HE WAS LEVEL AT 12000'. I REALIZED AT THAT TIME THAT I HAD A PROB. BOTH ACFT WERE IN A 'CST' STATUS; IF NOT BOTH; AT LEAST ONE WAS AND I WANTED TO ENSURE THAT I HAD GOOD READOUT ON THE SCOPE BEFORE TAKING APPROPRIATE ACTION. WHEN BOTH TARGETS WERE GOOD I SAW MLG Y TURNING INBND BEHIND MLG X. MLG X WAS LEAVING 11700' AND MLG Y WAS AT 12000'. I ASKED MLG Y FOR HIS HDG HOPING I COULD STOP HIM WBOUND TO GO BEHIND MLG X. MLG Y SAID HE WAS GOING THROUGH 300 DEGS AND I OBSERVED HIM ALMOST RIGHT OVER MLG X. I INSTRUCTED MLG Y TO TURN RIGHT HDG 360 DEG TO TAKE EVASIVE ACTION. ONCE MLG X WAS CLR I THEN PROCEEDED BACK IN WITH MLG Y FOR THE APCH. CALLBACK CONVERSATION WITH RPTR REVEALED FOLLOWING INFO. RPTR HAD RELIEVED THE INVOLVED POS ONLY MINUTES BEFORE THE LOSS OF SEP OCCURRED. HE BELIEVES THAT HE RECEIVED A COMPLETE POS BRIEFING BEFORE TAKING THE POS. AT THE TIME; PIT WAS MAKING ILS APCHS TO ONLY ONE RWY; 28L. AS RPTR WAS TAKING THE POS; THE OTHER RWY; 28R REOPENED AND IT WAS TIME TO START EMPTYING THE HOLDING PATTERN THAT WAS UNDER RPTR'S JURISDICTION. BTWN THE TIME HE TOOK THE POS AND IT WAS NECESSARY TO GIVE THE FIRST CLRNC TO EMPTY THE HOLDING PATTERN; SOMEONE (NOBODY KNOWS WHO) REMOVED THE FLT PROGRESS STRIP FOR MLG Y FROM THE `HOLDING ' BAY. WHEN RPTR LOOKED AT THE BAY; THE ONLY STRIPS THERE WERE FOR MLG X AT 13000' AND MLG Z AT 14000'. RPTR THOUGHT THAT MLG X WAS THE LOWEST ACFT AND HE STARTED HIM INBND AND DSNDING TO 9000'. NOT UNTIL MLG Y ASKED ABOUT HIS SEQUENCE AND STATED THAT THEY WERE AT 12000'; DID RPTR HAVE ANY IDEA THAT A PROB EXISTED. THE FACT THAT THE TWO ACFT WERE VERY CLOSE TOGETHER IN THE PATTERN AND THAT THEIR DATA BLOCKS WERE EITHER OVERLAPPED OR IN COAST CONDITION ONLY COMPOUNDED THE MISIDENT PROB. (CTLR'S EXPERIENCE LEVEL AND POINT OF CLOSEST PROX WAS DETERMINED.)