I would be surprised if Mass fails a car for multiple flash's alone, I would think it would be more so seeing readiness monitors in a (N/A) title instead of a ready title that would raise a flag. Dealers reflash cars all the time to upgrade ECU calibrations. When I worked at a dealer it wouldn't be uncommon to have over a dozen ECU revisions on one ECU part number, so if the inspection station was able to see an ECU was flashed a few times how do they know it just wasn't manufacturer updates that were also possibly done for better emissions....
As far as UPREV is concerned they offer a product to manipulate ECU code to make them tunable, I think that is their #1 priority as that is what sells it. If there is issues with specific states failing the vehicles that are UPREV'd I'm sure they will look into it when time allows.
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