When I start Claws Mail after restart OS, the messages those I have read before restart are back to Unread status. If I close Claws Mail before restart OS, app saves each status correctly.
This information is called "metadata". See Preferences -> Other -> Miscellaneous -> Metadata handling Claws Mail requires clean exits anyway, so ideally you should exit Claws Mail, and actually even other software before shutting down/restarting OS.