The native lemmy feature for this doesn't work. Maybe it's because my list is thousands of users / communities long. I tried several times and only a handful of these gets moved to the other account and it actually seems that me trying to move them crashes the entire instance.
Is there a lemmy app or some other alternative method to move these over?
Are you using the Import/Export Settings buttons in the settings page?
If you can reproducibly crash an instance then you should definitely file this as an urgent security issue in the lemmy repo so it can be fixed: https://github.com/LemmyNet/lemmy/issues