The latest version of Scrivener, 3.1.4.1, has fixed the root problem with nested indent settings corrupting across sessions. While it is impossible to retroactively fix lists in a manner that is not destructive (“messed up” indents look like custom indents for all intents and purposes), there is now a menu command that will reset list indenting back to factory defaults: Format ▸ List ▸ Reset Indents to Defaults. Use it without a selection to fix all lists found within the active editor (across Scrivenings), or select the lists you want to reset, first.
Run “Check for Updates” from the Help menu to fetch the upgrade.
