Right, and that isn't what they told the police, the first time. Only after court when it was clear that "it didn't happen" will never hold water, did they go back and amend that record with them.
This is literally how you get charged with "obstructing justice" --- you shut up or you tell the truth.
Are you talking about this part? It seems a pretty thin statement on which to rest an allegation of obstruction.
"The Uber department responded that they had no record of a trip from the vehicle with that license plate on December 5th, 2016, just after 11 PM, and the driver had not driven with them for 2 years."
This still leaves a lot of open questions and is IMO not even a compelling allegation of obstruction of justice, let alone proof. As I said before, it's entirely possible that the actual driver/car were not the ones registered with Uber on the account. It's also possible that somebody erred when looking up records, or a million other things.
What we do know is that by the time this made it to the first court date, Uber was not denying that a trip or a theft took place.
I'll reiterate my fundamental argument since this has strayed a little bit: this article is muddled and confusing with regards to cataloguing bad actions by Uber.
You can be damn sure Uber has a record of every Uber ride ever taken. Even if Uber had incorrect records in their database about which car picked up the rider, because the driver had e.g. failed to update Uber with their current car and plates, there is no plausible reason why Uber would believe that the ride itself had never occurred, because they have the rider's account information. They could have produced "rider account X requested a trip in Boston on such-and-such date, we matched that person with driver account Y, and driver account Y was registered in 20xx to Vernon Dudley, 4 Privet Drive, ...". But they deliberately didn't provide that information.
"this article is muddled and confusing"
Reality is muddled and confusing. Real life never has the clarity of an omniscient third-person narrator telling the reader the actual facts of the matter.
If Uber did their best to help the investigation then they could look up information not only by license plate, but also look at customer's account, look what rides were taken at that location and time.
This is literally how you get charged with "obstructing justice" --- you shut up or you tell the truth.