In Elfeed (Emacs RSS feed reader) with the Owncloud/Nextcloud protocol integration (via elfeed-protocol), I discovered that

(setq elfeed-protocol-lazy-sync t)

is necessary to keep read RSS articles in sync. Disabled (by default) it will update after the article is read in Elfeed, triggering what I think is rate limiting in newer server installs, causing articles to not be marked as read. Enabled it will update articles’ read status with the next update (article fetch).