Get it here.
“Synchronize” is now available when syncing with iOS devices for the first time. What happens is that if the data sets are completely distinct (as in created separately), they can be safely merged. If there is some overlap and some other issue causes the system to think the two devices have never synced before, a Replace sync will be necessary to restore good working order as before.
As a historical footnote, upgrading data from MacJournal 2.1 and before is supported once again.