UNAUTHORIZED RWY XING BY ACR. UNAUTHORIZED RWY ENTRY.

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WE WERE WAITING FOR OUR TKOF CLRNC FROM HOBBY TWR ON A DARK NIGHT WHILE HOLDING SHORT OF RWY 12R ON TAXIWAY DELTA AS CLRED BY GND CTL. THE TWR INSTRUCTED US TO TAXI FORWARD TO ALLOW SMA Z TO TAXI BEHIND. I TAXIED WITH CAUTION SO NOT TO CREATE JET BLAST FOR THE SMA AND NOT TO MISS THE HOLD SHORT LINE AS I DID NOT SEE IT IN THE DARK. I LOOKED OUT TO MY R AND SAW ACFT Y LNDG LIGHTS BEARING DOWN ON US ABOUT 2 MI OUT AND REALIZED WE WERE IN THE MIDDLE OF THE TOUCHDOWN ZONE ON RWY 12R. I IMMEDIATELY CLRED THE RWY TO AVOID THE LNDG ACFT Y CRASHING INTO US. THE TWR WAS BUSY WITH CONSTANT RADIO TRANSMISSIONS SO WE WERE UNABLE TO RELAY OUR SITUATION. WE STOPPED ON A TAXIWAY ON THE OTHER SIDE OF THE RWY AS THE LNDG ACFT Y TOUCHED DOWN. THE TWR CLRED US FOR TKOF ON RWY 12R WHICH WE DID WITHOUT FURTHER INCIDENT. LATER IN ANALYZING THIS SITUATION; I BELIEVE THE TWR THOUGHT WE WERE ON TAXIWAY ECHO WHEN HE INSTRUCTED US TO TAXI FORWARD TO ALLOW SMA Z BEHIND; OR WE MAY HAVE MISSED INSTRUCTIONS TO TAXI ONTO ECHO; OR THE TWR HAD INTENDED FOR US TO CROSS RWY 12R OVER TO THE OTHER SIDE IN THE FIRST PLACE. IN ANY CASE; MISCOMS OR MISUNDERSTANDING CAUSED ME TO TAKE EVASIVE ACTION TO PREVENT A MAJOR DISASTER THAT I AM NOTE SURE IF ANYONE ELSE SAW OR HOW IT EVEN HAPPENED. MY TAXI CLRNC WAS TO TAXI TO 12R VIA DELTA. SUPPLEMENTAL INFO FROM ACN 190689: OUR CLRNC INCLUDED INSTRUCTIONS TO CROSS RWY 12L; RWY 17 HOLD SHORT RWY 12R. WE WERE NOT GIVEN INSTRUCTIONS TO FOLLOW THE RED LINE OVER TO TAXIWAY ECHO SO WE CONTINUED STRAIGHT ON DELTA TAXIWAY TO THE HOLD LINE SHORT OF RWY 17. LATER WE HEARD THE TWR GIVE OTHER ACFT INSTRUCTIONS TO FOLLOW THE RED LINE TO ECHO TAXIWAY HOLD SHORT OF RWY 12R. WE HAD DISCUSSED EARLIER PRIOR TO THIS FLT; A BULLETIN THAT WARNED PLTS ABOUT BECOMING DISORIENTED AND LINING UP ON RWY 17 AND THEN TAKING OFF ON RWY 17 INSTEAD OF 12R. EVEN STILL WE ENDED UP ON RWY 12R WITH AN ACFT ON FINAL. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: RPTR PARTICIPATED IN STRUCTURED CALLBACK FOR RWY INCURSION STUDY. RPTR CLARIFIED POS AND RTE OF SMALL ACFT Z. SAYS THAT HE NOW REALIZES THAT ATC PROBABLY EXPECTED THEM TO BE ON THE 'RED LINE' TAXI RTE FROM TAXIWAY D TO TKOF END OF RWY 12R; BUT HE UNDERSTOOD TAXI CLRNC WAS VIA TAXIWAY D TO END OF 12R. BY MOVING FORWARD AT REQUEST OF TWR THEY INADVERTENTLY GOT ONTO RWY 12R AND DID NOT REALIZE IT UNTIL IN MIDDLE OF RWY WITH LNDG LIGHTS ON 2 MI OR LESS FINAL. ARPT CHART SHOWS RED LINE FROM TAXIWAY D TO RWY 12R; BUT RPTR THINKS THAT ATC SHOULD VERBALLY STATE THAT RTE. SAYS THAT HE HAS HAD ANOTHER BAD EXPERIENCE WITH HOU OP SINCE THIS INCIDENT; AND TOLD THAT STORY DURING CALLBACK.