When an update is released, please always check the Changelog first. Backup your saves (they should be in the Overwrite folder at the bottom of MO2), before you commit to any updates. Wabbajack doesn’t usually touch save files, but it does have the ability to delete them if it wanted to.
If you have added anything to this modlist at all, Wabbajack will also delete it. You should know how to stop it from doing this if you’re going to add stuff to modlists.