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.
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