Sometimes Pro/E doesn't need to regenerate features completely. If you've modified a chunk of a part that has nothing to do with certain features, all it really needs to do is restore your features (versus regenerating them again). This speeds things up considerably.
Sometimes though, you might change your part in such a way that Pro/E can't (necessarily) make the same assumptions, so it has to regenerate the features again.
It shouldn't be a major cause for alarm. Pro/E is just telling you "I'm regenerating this hole, not restoring it"
