B747-700 Captain reported a difference in fuel used versus fuel totalizer in flight. The Flight Crew rechecked their fuel numbers and elected to divert and make a precautionary landing.

Narrative

This is a copy of an incident report; but new info prompted me to submit [this] report; new info on bottom of report: We left ZZZ with 4;000 lbs. extra fuel; on a re clear flight plan that left no drop to spare. I had noticed in the company NOTAMs that the fuel bias was only 3.5%; compared to Aircraft Y's 7.7%. Must be a good airplane; I have not flown it yet. I followed the flight plan's CI30; and step climbs. Yet slowly we started losing fuel. Our re clear point was ZZZZZ; halfway between ZZZ1 and ZZZZ. I got woken up by the operating crew as we were 1;500 lbs. below the flight plan required fuel; and Operations had told them to turn back to ZZZ1 for fuel. This flight was the first re clear Dispatch for this flight follower. We lost 5;500 lbs.... and a look at the Progress page 2 confirmed a 2;000 lb. discrepancy between Totalizer fuel and Calculated fuel. When we reached cruise Calculated was actually lower than Totalizer; so the loss was really more than the 2;000 lbs. Headwinds had been stronger than flight plan; eventually bringing us 5 minutes behind planned time. I asked Operations if we could go to ZZZZ1 (northern ZZZZ; which we used to use for re clear flight plans and ETOPS alternate) with ZZZZ2 as alternate? Better there than returning to ZZZ1. How is the weather in ZZZZ3; can we use that as destination alternate instead of ZZZZ4; and maybe; possibly prevent a diversion altogether? ZZZZ3 is at minimums now; ok; how for when we are supposed to get there? From an hour before? Good; weather at ZZZ? Good. Ok. How much fuel do we need? He gave me a number that was much higher than we had on board. I am trying to translate all these lbs. numbers in kilograms; lbs. don't tell me anything. We need 7 Tons at alternate.. times two plus a little bit equals 15;000 lbs. How much to go to alternate? 10;900 and some; ok; 26;900 lbs.; plus 70;000 to get to ZZZZ2 = around 100;000 lbs.; 8;000 less than with ZZZZ4 as alternate. Those are my numbers; quickly calculated in my head; in confusing lbs.; without the prerequisite amount of coffee... Operations numbers are way higher. But they come close when the ETP's are removed. Yes; we are already at our ETP's; no need for them anymore. We need 98;000 lbs. for ZZZZ2 with ZZZZ3 as alternate. The entire crew is happy with the new numbers and we agree on the new plan. What I also noticed a lot later was 4;000 lbs. of fuel in the center tank; 2 Tons that should have been scavenged out. Turning on the Center tank pumps made no difference; but it did create nuisance messages. We landed with 29;000 lbs.; a lot less than the 35;000 we were planned to land with. If we had to divert to ZZZZ3 we would have landed with less than 14;000 lbs. (6 Tons) usable fuel. What was the saving grace in this whole event was that we had a delay of 3 hours in ZZZ; and the forecast for our arrival was now better than what it would have been at our originally planned 0615 ETA. ZZZZ2 was at minimums; ZZZZ3 below alternate planning minimums; so yes; without the 3 hour delay we would have diverted; more than likely been out of duty time; and ran into the curfew at ZZZZ2; pushing us even further back. New information: [when] the airplane got grounded in ZZZ1 after a Mechanic observed a fuel leak. Consequent investigation found broken; leaking fuel lines and internal fuel tank parts missing or broken. This explained losing fuel and the uncommanded transfer of fuel back into the center tank. This aircraft sat in the desert for many years; retired by its former owner and joined our fleet at the end of [the year] after a heavy check. These parts might have been removed during decommissioning of the aircraft or during its time [while not in use]; however; during the heavy check these missing parts were not checked for.Cause might be missing; broken parts that were not detected during heavy check.Check fuel tanks during heavy checks.