Here are the marks that I should use to distinguish important articles in my gnus mail client:

• persistent (* mark): important articles that have to stay at hand ("treasure" articles)
• ticked (! mark): articles that I've partially read, but that I've yet to process (reply, or read more deeply)
• dormant (? mark): articles that I want to show up if there are replies in the same thread

See matching entries in the Gnus manual:

• Persistent Articles (Gnus Manual)
• Unread Articles (Gnus Manual)
• Limiting (Gnus Manual)

If the articles count or list gets wrong in Gnus with the nnml backend (for example because of full disk), it can be rebuilt this way:

M-x nnml-generate-nov-databases

A more generic way is to go in the Server buffer (^ from the Group buffer) and use g to regenerate all its data structures.

Also try C-u M-g (gnus-summary-rescan-group) from Summary buffer to rescan the group for new articles.

• nnml Mail Spool (Gnus Manual)
• Server buffer (Gnus Manual)
• Server commands (Gnus Manual)
• Exiting the Summary Buffer