Those messages alerting you to works are shown with any train going over a route affected, even if the train itself is not affected. This so people know why the schedule they see is not the usual one.
Note that if you miss your connection in Domodossola you can just hop on the EC that follows, as in Switzerland that train has no compulsory reservation.
Note that I would have booked the EC at 15:10, that still has seats…