Default / typical behavior is for mutt to update the mailbox message state (new, unread, read, replied) when closing the mailbox. Using the -R flag prevents this behavior.
Forgetting to do so is more an annoyance than an End of the World Event, but it's an annoyance which can be avoided with a really simple flag use.
It's something I read when I was getting started with mutt.
Perhaps is much less of a deal than I thought, after giving a cursory Google I can't seem to find what I read that gave me that impression and I don't see any major warnings not to.
Like the original poster, I'm using offlineimap and maildir's entirely.
What kind of conflicts do you get?