When the "Replace Server Data” method is used with CalDAV and it ends up creating duplicate lists - that mostly just means those lists are "Shared Lists” that have been marked as read-only by Reminders. This sadly happens as Reminders marks them read-only but does not return an error to 2Do and so it ends up creating duplicate lists for the same name. There is no "clean” solution to the issue as CalDAV will repeatedly create a new List called "Home” (for example) as many times as you try and replace data on the server. 

The solution to this is more of a manual one. The Replace Server Data method should work in general, however after it ends up creating tons of duplicates (depending on how many times you tried), simply log onto www.icloud.com (or use Reminders app) and then manually delete the duplicated lists from from there, or temporarily disable sharing on those lists. Now sync 2Do again and it should sort itself out. If it does not, try and delete the same list from 2Do.

We sincerely apologise for the inconvenience but such annoyances can be part of syncing with Reminders over CalDAV. We do highly recommend you stick with Dropbox sync, but in the unlikely event of going through such an unpleasant process, sadly the only way forward is manual intervention. We hope this information helps, if not, please don’t hesitate in contacting us.