iBooks stopped syncing reading progression, bookmarks and notes between my iPad Pro 10.5 and iPhone X - started happening within the last 1 or 2 betas. Signing out of iCloud and signing back in on iPad had no effect.
Also, removing the book (“Remove download”) and re-downloading it (from both devices) resulted in restoring their respective progression - e.g. the iPad restored its own progression (bookmarks, notes, etc.), while the iPhone X restored its own separate, different progression.
I don’t think iCloud is confused about having multiple copies of the same book - for the books I tested, they only appear as a single entry in my Library.
It feels like iCloud is keeping track of reading progression and bookmarks for each book separate by device. I really hope this is not intentional.
Update: This issue (at least for me) affects both iBooks store-bought books, as well as my own manually added .epub books.