I am only ending my first year of beekeeping and have NO top bar hives, so take this for what it's worth:
If the hive was innundated with flood waters (carrying silt, ag and household chemicals, sewage and who knows what else and is still wet I would take it apart (setting the bees aside carefully in a suitably ventilated container) and scrub it out and let it dry open in the sun before re-hiving the bees. This advice comes from my years of volunteer work as a disaster specialist for the Red Cross. It's not just the water, it's what the water was carrying that is the worrying part. If it is really gross (and even if it is not visibly groos, but you are in an suburban/urban area where the storm drains flooded) a little Clorox in your scrubbing water won't hurt. (I regularly soak the insides of my hive-top feeders with hot water and little - a couple of tablespoons in 5-6 gallons of water - Clorox to remove the moldy spots and freshen them up. Bees also will drink from swimming pools so a trace of Clorox is not a bee-killer. Rinse copiously with clear water, afterward.)
As to what temporary container for the bees: think of something shaped like a nuc box or a swarm trap, with lots (more is better) of holes. Staple in supports for comb if you have them and they are salvageable. Other wise just something for the bees to cluster on around the gourd with the queen in it. (Gourd should obviously fit inside the box!) Make sure they have a suitably sized hole to go out. If weather conditions permit I would park it back where the hive was before. The size of box I'm thinking of is the size that bulk copy paper comes in at an office supply store. Or the size of one of those fold-to-assemble paper file boxes. Make lots of holes (If you think you've made too many, you can close them or screen them, but the reral danger is overheating, I think.)
I'm not sure how you were feeding: open or from some kind of in-hive feeder? If in-hive, then get a second box and arrange it so the bees can get up into it to access the feeder. (Don't worry they won't lose their topbar chops in just a few days of emergency arrangements. But you could also try to get a big produce box that might be closer to topbar dimensions. But don't make a big deal about. Get adequate hiving for them for the next few days. Concentrate on getting their own hive cleaned up, dried out and ready. And hope for the best.
What I would not do is confine them into a wet, uncleaned hive. If you have power you could even set some fans on it to dry it out faster after washing it thoroughly. Afterward, can you arrange to have the bees in a reduced-sized area of the top bar using follower boards? If so I would drill extra holes in the unoccupied parts to facillitate additional complete drying out. Do not let closed, even slightly damp spaces fester into mold.
I think your bees may surprise you and recover well. If not you've done all you could, which is some consolation. But I will keep my fingers crossed for both you and the bees. Please update when you can. (Just so you know someone else recently posted about hives being innundated and I was surprised and happy to read a week or so later that they were doing OK. So keep that thought in mind!)
Enj.