The only issue in this story is that the author doesn't mention if it was the HP or LP fuel filter, but it's most likely to be the LP filter.
The 'discovered during routine maintenance' issue: It is entirely plausible! Assuming that there were no EICAS status messages, no flight deck effects, no maintenance memos, and no reports of abnormal behaviour from the crew (airplane's behaviour!
)... then one can only assume that the plane would keep flying until it was grounded for routine maintenance such as an A-check. (Fuel filters are replaced on A-checks, not service checks or earlier).
At this time, an unsuspecting mechanic could easily open up the LP fuel filter housing and discover that there never was any filter installed!
On older trents (T700/T800), the fuel/oil heat exchanger assembly houses the LP fuel filter. Now, if you replaced one of those, it comes from the factory WITHOUT the fuel filter pre-installed. It's quite possible that the T1000 is the same.
I know so, because it's happenned in my previous company, and several planes flew perfectly well for up to 3 months before it was discovered - again - during routine maintenance! Lesson learnt!
Having said all of that, blaming Boeing (and not the fuel filter vendor, or engine manufacturer) is the right thing to do... not because Boeing's ethically ultimately responsible..blah blah... but because it's most likely that they opened up the fuel filter and forgot to put it back.
I say so, because after every major job performed inside a fuel tank - repairs, component replacements, leak checks (from inside), etc - it is policy to replace the LP fuel filters after a few hours of engine operation, just so that if you do leave anything in there, and it gets caught in the filter, you have a chance of getting it out quickly, and leaving a nice clean new filter for when the airplane resumes normal operations.
I would think that BUILDING the damn tank/wing is a major job, and Boeing would have a procedure to replace the filter after the first few engine runs.
At the end, it seems exactly like a Boeing QC/QA issue. Too much of this airplane has been outsourced, literally and figuratively. I've found boombox radios, flash lights, tools, etc., inside 777 pylons, fuel tanks, and empennages.
Let's hope with the 777X, the airplane manufacturer actually starts manufacturing airplanes itself!