We had that happen one time due to Delta having issues and us having them move us to an AA flight. Worked out well for us as it ended up being direct, but our bags didn't make it.

Wasn't a big deal except it was January and I didn't bring a change of clothes in our carry on so I was wearing jeans and rather hot. Fortunately however our bags arrive the next morning. We just had to take a taxi to the ferry dock to get them.

That was the last time we used the ferry, not entirely because of this, but in part. With prices being pretty similar for us, its easier to not have to worry about this - had we flown into EIS, bags would have been delivered to the moorings base. Needless to say, I always have some extra clothes in my carry on now