Sleeper car and tansfers

The Deutsche Bahn website (my go-to information source because it is so user-friendly) does show that you must change trains in Breclav.

Are you aware that the second train makes five stops before it gets to Krakow? Those stops come at 1:32 AM, 3:18 AM, 3:39 AM, 4:08 AM and 4:50 AM.

Unless you are the sort of folks who can sleep through anything, it will not be a restful night. The last time I took a night train (in a completely different part of Europe, so I suspect your experience will not be as bad), I did not get one wink of sleep the entire night, and I lost the following day because I was so wiped out.

When new schedules come out for the season, as they did recently, it often takes a while for the Budapest-Bratislava-Krakow night train route to show online as one continuous train instead of two. It's been happening for years, since the train numbers change and train cars may get shuffled with not all making the whole trip. When I look at the current winter/spring schedule however, that's been resolved. So look again at DB.

It looks like those are two separate trains. EN 476 originates in Budapest while EN 40456 originates in Vienna (Wien). It looks like the trains might be combined for a few stops between Breclav and Bohumin, then run slightly different times to Krakow Glowny. The final destination for both is Warsaw, but EN 476 gets there about 25 minutes later. If you look at the Bahn website, it looks like you can stay on EN 476 all the way to Krakow and only get there two minutes later than if you change cars (and compartments) in Breclav.

Oops. I looked at the current schedule since no date was specified in the original post. I'm glad the trip is occurring later, when there is at least no train-change to worry about.

From Brataslava, have you considered taking a bus 30 miles to the Vienna Airport and flying non-stop to Krakow on Austrian Airlines? Saturday and Sunday, the fares are 89 and 78 Euros. Tuesday, Wednesday and Thursday, the fares are around 124 Euros.
I'm only good on a train about 3 to 3 1/2 hours. And I'd really not want to take a night train anywhere.

And I'd really not want to take a night train anywhere.

I really have to post a counter argument to Davids post. I've had thirteen nights on night trains in Europe and in the US, and I've never had a problem sleeping. Last year, my partner, who had never had much experience on trains, was with me on an overnight train from Reno to Denver (Amtrak) and she thought it was a wonderful experience.

You get on the train in Bratislava around 10 o'clock at night and arrive in Krakow around 6:30. If you can sleep on the train, you've just used 8½ hours of otherwise unused time to get to Krakow.

If you fly, the only reasonable flight I see on Austrian Airlines (others take 8-16 hours) is about an hour flight from 1:10 to 2:10 in the afternoon. The latest Flixbus connection which will get you to Vienna in time for your flight leaves Bratislava at 10:35, and that's pretty tight. 9:30 would be better, so you will not have any quality sightseeing time that morning. If you get to Krakow at 2:10, find the bus into Krakow (it takes an hour), you can't expect to get into Krakow before 3:30 or 4:00. Essentially most of the day is lost. Then you have the cost of a hotel in Krakow that night to add to the cost of the flight plus your hotel to Flixbus in Bratislava, Vienna Erdberg to the airport, and the bus from Krakow airport into town.

After the train leaves Breclav just before midnight, there are only three stops, one for 1:39 in Bohumin before 4 am.

I'm only good on a train about 3 to 3 1/2 hours. And I'd really not
want to take a night train anywhere.

I'm with you. Plus, we feel gross not showering; a sponge bath at a sink is not comparable. I've taken overnight trains and never again. I'd rather fly or save the destination for another trip.

No problem taking the night train as an option. On my trips I factor in 1-3 night train rides, just as on the last trip in May three rides at night.

Doing that option the night train has to meet my expectations, ie, a direct connection startiung at 7 pm so that I need not transfer say at 3 am, arrival at sometime between 6 to 10am, even though 5 am in the summer is all right too. In your case boarding at 2200 hr and arriving at 0600 would be ideal.

If you feel gross not showering, then book a compartment with shower and the problem is solved. https://www.seat61.com/international-trains/trains-from-Krakow.htm#Krakow_to_Budapest