Apple Mail doesn't provide a built-in mechanism for marking emails as replied (or clearing said mark). I solved this weakness with a simple AppleScript that operates on whatever messages are currently selected. Simply create the following script using the Script Editor, and save it to Library » Scripts » Applications » Mail in your home directory, or in /Library » Scripts » Mail Scripts for use by all users.
This script marks the selected messages as replied to:
using terms from application "Mail" tell application "Mail" set selectedMessages to selection repeat with eachMessage in selectedMessages -- set was replied to of eachMessage to false set was replied to of eachMessage to true end repeat end tell end using terms fromFor marking as unreplied, I used the brain-dead solution of simply creating a second script which is identical with the exception of substituting the value false into the set was replied to line, as demonstrated by the commented line which starts with --. Save the two versions of the script to one of the above folders.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20091101034608640