Update 7/10/15: I have confirmed that the Porter Square location is permanently closed. Their Brookline location is still open.
I tried to stop by Japonaise Bakery in Porter yesterday when they should have been open but was greeted by steel doors. I called the main store in Brookline today and was told that Porter was closed due to equipment issues. I asked if the closure was permanent and was told she hadn't decided yet. I told her that would be too bad. It wouldn't surprise me if they close permanently since they never have very many customers. It would be a real shame. Japonaise has been in the Porter Exchange for as long as I remember but it seems like they've struggled for business since moving to this less visible location (they used to have a kiosk in the main hallway outside Bluefin). I'm sure that Kotobukiya's closure has hurt them as well.
Update 3/19/15: Stopped by the Brookline location today and found out that the equipment that broke is used to make their bread so they had no bread or bread pastries (other than bread pudding), just cakes, flan, a lone tray of almond croissants, and a few onigiri. It seems they are also struggling with being understaffed. They are hiring for all positions.
Update 3/20/15: Went back to the Brookline location today and they had azuki & ichigo creams (yay!) along with a few other pastries but still no bread and no word on when the equipment would be fixed.