In the Finder, when you replace one folder with another, the old folder is deleted. On Windows, the two folders are merged. (For reasons I’ve never seen anyone even attempt to explain, Windows calls this action “replacing”.) This difference often bites switchers — regardless which way they’re switching — who are accustomed to “their” way and are surprised by the other way.
Matt Mullenweg is a somewhat recent switcher from Windows, and he just lost a folder full of photos because he assumed the Finder considers “replace” to mean “merge”, as it does in Windows.
Which reminds me of my proposal from two years ago, in “I Love It Because It’s Trash”, which is that when the Finder replaces a folder or file, it should move the replaced items to the Trash instead of instantly nuking them. Not only would this eliminate catastrophic mistakes, but it would also allow replacements to be undoable. I’m still convinced this is the way things ought to be.
(Unsurprisingly, I dislike Windows’ “merge when replacing folders” behavior. The main reason is that when you replace a file with a same-named file, Windows does the same thing the Mac does: it deletes the old copy and replaces it with the new one. It’s a terrible idea for “replacing” to mean two entirely different things, depending solely on what it is you’re replacing.)