Yes, guaranteed connections booked using Multi-City are still guaranteed. Some things have to be booked using Multi-City, particularly between smaller cities that haven't been added to the city pair lists between two trains that show as guaranteed between larger cities.
While that isn't the cause in your case, the agent probably found it easier to just modify one segment, so it now comes up as Multi-City.
You may feel easier knowing how misconnects actually are handled. The computer spits out a list of passengers on the inbound train that are booked on the outbound train which will be missed, on the same reservations. Amtrak agents then work the list to set up accommodations and revised itineraries for the affected passengers. It doesn't matter how the reservation was made, only that both trains are single reservation so the system can find it.
The times that Multi-City doesn't work is when it is used to force connections that aren't otherwise guaranteed. That's primarily because no one will run or work such a passenger list. The converse, different reservations on a guaranteed connection, doesn't work either. That's because, while a list will be generated, passengers having separate reservations won't be on it.
