This will never happen, and I say this as someone who has been involved in planning and funding of projects like this in Concord and having spoken to Concord's town staff about this exact idea. The opposition that would come from the Nashawtuc Hill neighborhood to reestablishing the bridges and having the rail trail pass around the base of the hill would be intense to say the least. It would be like proposing a highway over Beacon Hill--there'd be Superbowl ads in opposition.
I used to occasionally use the Reformatory to bike commute, and at the time it was in pretty bad shape through Concord, so I dreamed of it one day being paved, and being connected to the BFRT as a key element of the regional bike network. In the years since, through the work of really one guy and maybe a handful of others, the trail in Concord has been improved by hand so there's much fewer mud pit sections. Its now pretty easy to bike down, and I've grown to appreciate that there's a case to be made for keeping the trail unpaved as it passes through the national wildlife refuge, though I'd like to see it consistently graded and surfaced with stone dust, more like the Narrow Gauge Rail Trail. Critically, where it passes across Rt. 62 needs to be fixed, and the Bedford plan, if salvaged, would do this.
It's my suspicion that the latest turn-about on paving the trail in Bedford was spurred by folks from Concord. Bedford has consistently supported paving the trail for 10 years, but recently there was talk in Concord that with the improvements coming to the Bedford section and work on the Concord section of the BFRT wrapping up, now it's time to turn to paving the Reformatory in Concord. There are some folks in Concord that live along the Reformatory that are militantly opposed to any project of any kind that cuts any trees, and they freaked out about this talk, and I believe then worked to get people in Bedford opposed to the already-funded Bedford paving plan. The language of the Bedford opposition around clear-cutting is a clear echo of Concord concerns. Unfortunately, the pro-pave folks kept pushing their idea without apparently appreciating that they were poking the bear, and asked for money to study the idea at Town Meeting. This triggered the opponents to propose an article doing the opposite, namely, preserving the trail as is in perpetuity. The former article failed and the latter article passed, and so now it is the established position of Concord that the Reformatory should be left as is. There are some platitudes around making the trail more accessible, but I'll believe it when I see it.
I think the best outcome at this point would be: the Bedford plan is revived and results in a tunnel under Rt. 62, the Concord section gets a stone dust treatment, and one day we get a better connection (maybe rail with trail along the MBTA line from Concord to West Concord?? A fella can dream...) from the existing terminus of the Reformatory at Lowell Road to the BFRT in West Concord.