The upgrade to 2.3.2 to 2.3.3 is a minor (but important) update, only 5 files were actually changed. A security problem was found that forced the release of 2.3.3 quickly to fix it.
However, as far as a general upgrade procedure goes, you would usually remove the wp-admin and wp-includes folder entirely (assuming you have not made any custom changes to the core files), and then upload the new stuff. The only “overwriting” you’ll get in that case will be the default and classic themes, along with the akismet plugin. Assuming you don’t use the default or classic themes, then it doesn’t matter much whether you overwrite them or not. Akismet will be upgraded probably by you overwriting it with the latest one. Some stuff in the root directory will be overwritten as well.
Generally, we don’t like to recommend overwriting files via FTP here, because, for some reason, people have proven to be very bad at it. I don’t understand it myself, but countless people come in here saying that they upgraded but it still says the old version… This means they did not actually upgrade, and trying to convince them to try the upload again is usually an exercise in painful and annoying futility…
Anyway, in theory, a straight overwrite would work all around. But people suck at that, so a clean sweep of the main two directories is usually enough. These are also the directories that occasionally get files removed or renamed from version to version, so cleaning out older versions is generally a good idea.
