Here's what we know (about Framingham-Worcester):
P529 is cancelled. That train usually carries about 741 passengers. They probably will go to P531.
P583 is cancelled. That train usually carries about 873 passengers. Do they leave early and get on P527? Or go to P531? Either option is problematic.
Plan on getting on all other trains at Back Bay. Some trains might be able to start at South Station, but it won't be reliable to expect that. They have to get manually switched out of South Station and thru the non-functional interlocking at "Tower 1." Some trains will probably just originate at Back Bay - never having gone to South Station (perhaps all day).
P527 usually has about 1227 passengers on a train with 8 double deckers. That's a capacity of about 1440 seats. But who knows if that set is in position to make that run. If it gets any passengers from P583, it will be crushingly overcrowded.
P531 usually has about 504 passengers. Who knows what size set they use for it - maybe a six double set? That would be a capacity of about 1080 passengers. If it gets passengers from both P529 and P583, it could also easily become crushingly overcrowded.
Another way to look at it: From 5 PM to 6 PM, usually outbound load is 3,345 passengers. With 2 of the 4 usual trains cancelled, it will be very ugly tonight.
Leave early and expect overcrowding and big delays. And remember it isn't the fault of the conductors. Give them a break.
Friday morning will be a problem - even if the "Tower 1" problem is fixed, the train sets will be out of position, and there probably aren't enough hours or crews to get everything reorganized in one night (esp. if Tower 1 is still not working).
This blog has some great logistical tips: