We'd asked about this earlier this month, and we just now discovered another big list that had been nuked.
We're running the latest version of everything, but I suspect one additional plugin we have may be conflicting. That is wp-optimize. It has a setting to remove "transient" options from the database, and when I first installed it I ran it with that box checked. Looking through the backups, I see that there are options labelled _transient that have to do with subscribers. So, when those options -- which seem to hve to do with deleting subscribers -- were removed something triggered all the subscribers disappearing.
At least that's my theory. Can you please investigate? We do need to optimize our rather large database sometimes, and can't manually go through table-by-table. Thanks.