Are you sure that there’s no Smart Group Indexed Item in Inbox below the ones shown in your capture? I guess DEVONthink just selected the instance of Indexed Item in Inbox in Smart Group .Recent Inbox Added This Week excl Subgroups copy because the latter got a period at the beginning of its name, i.e. it’s sorted above Indexed Item in Inbox.
Selecting a random instance of a record does happen after deleting a replicant, maybe it’s the same behaviour in your case.