Well, considering that US 10 wasn't truncated when the SS Badger and her sister ship the SS Spartan stopped running before, I don't think they'd have to truncate it this time. The Chessie System ended in 1983, and those two ferries were idled. The Badger wasn't put back into service until 1989. Oh, and in further support for "no change", the Wisconsin port during the Chessie system wasn't Manitowoc, it was Kewaunee. US 10 wasn't routed any differently at the time, which tells me that ferry service isn't strictly necessary. (The two sister ships were designed for ice-breaking capabilities, but Lake Michigan Car Ferry doesn't run the Badger during the winter.)
That said, given the National Register of Historic Places designations the ship carries (she's the only, or one of the only entries listed for two states) and her designations as a National Mechanical Engineering Landmark, we don't know what will happen. There is a group fighting to make her a National Historic Landmark, which could stop the EPA's regulations. A bill in Congress, and an application by LMCF could result in an extension of any deadlines to make changes.