I built the teleporter in Sanctuary Hills and used it to get into the Institute. The settlement was later attacked and the teleporter was damaged. Unfortunately, because it's a unique building, it cannot be repaired.
I understand that the teleporter is necessary in the future if I want to choose the path of destroying the institute with the Minutemen, so it needs to be operational.
Is there some way to repair it? Especially convenient would be a simple console command (PC version) to repair settlement objects, which I wasn't able to find.
Best Answer
I've finished the game with each faction at least once, and I've done very nearly every side quest in the game with one character or another.
You don't need the molecular relay again for anything ever, it is always damaged after you use it, and I don't believe it can be repaired.
In the final Minutemen quest, you'll use the relay inside the institute, not the one you built in your settlement.
Furthermore, if you ask the tech person about testing the relay before the first time you use it, they will tell you that it is only going to work once.