Hello,
My husband and I will be visiting Prague, Krakow and Budapest in the next few weeks. I plan on taking some capris and slacks as well as a couple of skorts.

My question is regarding what is appropriate to wear when visiting churches. Will the skorts be OK, or do they require knees to be covered?

The only church with any sort of enforced dress code was Budapest Cathedral, where a man at entrance was handing out a piece of nylon cloth to females wearing shorts or short skirts/dresses, which they were expected to wrap round their waist.

Never heard of any dress code in churches in Poland or the CR. Capris and long pants will be fine. If they required knees to be covered, that would rule out many women's regular dresses and skirts, so no, there is no such rule. Not allowing short shorts or very short skirts (common sense is you shouldn't wear such a thing) apparently in Budapest isn't the same as not allowing knees to show.

I had to wear a shawl at St. Mary's in Krakow because I had a sleeveless dress on. They supplied (rented?) these little shawls at the place you got entrance tickets. I don't remember anything about knees, sorry--was wearing a knee-length sundress.