[dnanian]

Hi, Tom. It reindexes because the index is not preserved across copies. If you don't want it to index your backup, you can add the backup drive into the Spotlight Preference Pane's "Privacy" tab.

If you do a temporary start from a different drive with Option, it'll switch back to the default drive the next time you restart. You can check you current startup drive in the "About This Mac" panel.