It should be noted that public broadcasting stations (like PBS) have a different set of rules than commercial stations, that instead of being based on DMAs, they're based on whether the signal is within 50 miles. Markets can have as many public broadcasting stations as there is demand for, so there will be no concern at losing WGBH or WGBX in the Providence DMA, along with WSBE.
As for commercial stations, typically there is much stronger protection for the netlets (networks not affiliated with NBC, CBS, ABC or FOX) in regard to duplication, mostly because these networks are much more dependent on syndicated programming to fill out their schedules, and are weaker in general. However, WHDH being independent should likely prevent it from being removed as long as it remains considered significantly viewed in Bristol County, MA. They are, however, subject to non-duplication rules regarding any syndicated content they may carry being blacked out to preserve the rights of whatever Providence stations may air it.
This is likely going to continue going forward. Local broadcast stations are very expensive, and a similar deal happened between Comcast and Nexstar last year, which removed duplicate affiliates. Both Comcast and broadcasters support removing these for various reasons. Nexstar had their stations used in a previous dispute by Time Warner Cable for various affiliates. Comcast gets to keep broadcast fees down for what is largely solely carried for local news that can be found online already without customers having to pay for additional stations that mostly will be blacked out, both from network and syndicated programming going forward.
While customers may not be happy, I don't see any way around this being the future for all duplicate market affiliates. Sinclair, Nexstar and Hearst have already provided exclusivity deals. The only situations where this will continue is with state/local officials intervening in my eyes, as well as situations where the market and the neighboring market are both owned by the same company. For example, where I'm originally from in MD, Comcast carries both KDKA out of Pittsburgh and WJZ out of Baltimore, both of which are CBS owned and operated stations.
