In a vacuum, you're right -- it's confusing. But I'm going to go out on a limb here and guess that Flores watched the previous 2 games and came to a different conclusion from the start of the season.
As far as we know there was an open QB competition and Fitzpatrick won. Unless you have some insider information I can only base my opinion on the facts presented.
No I'm saying your theory of not risking his valuable asset due to a crappy OL makes no sense since he literally risked him 3 games into the season. Let me propose an even crazier theory--there was an open QB competition--Fitzpatrick looked better in camp--Rosen didn't look as good in camp--Fitzpatrick won. Obviously with the offense struggling and Fitz stinking it up Flores decided to go with Rosen to see what he has. He has 13 more games to show us what he has.