That's what I thought. It would have made more sense to have run Stevens.
I also forgot to mention that the rumour as detailed in that article is that they only had one copy of the software. That's really hard to believe, as software is pretty darn easy to copy and paste. If they'd said they only had one licence, I couldn't maybe believe it, but in doing so I'd also have to believe that Lowdon, Booth, and co are supremely stupid individuals for not buying a licence that allows them to use the software on both cars at the same time. More to the point, as others already mentioned they could have still qualified both cars if it was merely a software licence issue that kept Stephens out of qually.
At the end of the day, most of the time the simplest answer is the correct answer. And in this case I'd suggest the simplest answer is that the problem that sidelined Stephens is exactly the problem the team have said it was, with the fact they're on a skeleton crew from a staffing perspective making it impossible for them to strip the car, find and fix the exact fault, and rebuild the car in time. Keep in mind here that even the big teams took a large chunk of last year before they could turn around a major fault repair quickly. Even now, with the complexity of these cars it takes a lot longer to strip down and rebuild than it did prior to 2014.
Could further add that of the quotes used in that latest article to help give the rumour some credence, the leading one is from a man / team (Fernley / Force India) who are far from unbiased in this matter. Fernley has so far, in my opinion, done everything he can to throw roadblocks in front of Manor's comeback - because, no matter how little they'd get, they need every single pound they can get and Manor going down is a quick and easy way to get a few million extra.
I'm still wondering about the exact circumstances of the vote where an apparent request by "Manor" to run the 2014 car was refused. Manor have claimed they never submitted the request as they were already in possession of a letter giving them the concessions they needed. Did someone else submit it on their 'behalf' in order to be able to reject it and nullify the letter? Why did Fernley go so hard into the press putting a downer on Manor's "application" (that Manor claim to have never made) indicating it was refused because it didn't include information that at that point was still highly confidential and therefore couldn't be shared?
Let's face it - if a rumour surfaced tomorrow that Force India were the ones who lodged that 2014-car application, and seeded this latest rumour, then that rumour would be just as believable as the current "Manor can only run one car" rumour. It would be very, very difficult to prove or disprove.