Here is a small mutt macro that marks all tagged messages in the current folder as read (removes flags N and O).
macro index "<tag-prefix><clear-flag>O \ <tag-prefix><clear-flag>N \ <untag-pattern>.*<enter>" \ "Mark tagged as read"
Basically, it removes the flags O (old) and N (new) from all messages that are tagged.
For marking all messages as read, see earlier post: /blag/mutt-thread-collapsing-made-easy.
|'||Mark all tagged (old and new) messages as read|