Support

You are right. Admin Tools cannot handle references to other tables in VIEWs, FUNCTIONs, PROCEDUREs, TRIGGERs or foreign key relations. This requires dropping and creating afresh the tables, in a specific order. The only way to properly do this is using Akeeba Backup Core or Professional to backup and restore a site on the same location, choosing a new prefix during restoration, then removing the old tables.

The change prefix feature in Admin Tools was written back in the Joomla! 1.5 days when this kind of database entities were not used by the vast majority of extensions. That was back in early 2010. I think that at that point even Akeeba Backup didn't support advanced database entities except some for a rudimentary VIEW support. I think the only right thing to do is to remove this feature from Admin Tools along with the other similarly problematic feature which changes the collation of tables (also best handled by Akeeba Backup Core and Professional).