There could be a read flag associated with each chapter number, rather than just each groups individual version of the chapter. Then when an alternative version of an already read chapter is released it could be hidden from 'Latest Updates' OR displayed differently like, greyed out text, or a 'You have read alternate version' label. This would also work for reuploads. But it may still be a problem if a chapter/volume number gets changed or if a multi-part chapter gets combined into one (ex c5.1 & c5.2 become c5). Perhaps read flag could be linked to a unique ID tied to each chapter number.
Another simpler option would be to track series 'progress' (Highest number volume & chapter read), then just display it somewhere on the 'Latest Updates' entry. This way reader can tell at a glance if they may have read it, with out have to check check series page. Though again, if chapter/volume number changes it may be an issue. (I'm not suggesting this progress value be used to hide anything as it obviously be an issue when older omake chapters get added)