Needing to reconfigure how assets are set up on a Craft build. Is there any way to bulk remove assets without breaking entries that are already referencing these assets?
Not sure if this helps at all, but you can easily bulk remove assets by physically emptying the associated asset folders then going to
settings: update asset indexes. This of course may break your entries.
To avoid this you might try setting up a parallel assets group with the correct settings, copy the assets in question over to the new folders manually, update asset indexes for the new asset groups, and then change the corresponding entries to reference the new assets (either manually or en masse via plugin). Once the entries are updated, then you can delete the old asset groups.
If you just need to move/rename the folder and not adjust the relative hierarchies, then you should be able to just change the settings on your existing asset groups, rename/move the folders in question, and update asset indexes. This shouldn't break any of the asset links (provided you don't save any entries in the interim).
Back up your database!