I was incorrect about the battery issue going away. Deleting the ISD file did correct my CIVA navigation problem though.

My start-up goes as follows (parking brake set):
1. Power-up the CIVA unit.
2. Enter aircraft position coordinates.
3. Load AWC file.
4. Align CIVA (fast align).
5. Load ADC file while aligning CIVA.
6. Switch CIVA to 'Nav' when green light illuminates (accuracy '05' or lower).
7. Change both rotary switches on engineer panel to 'Gen 2'.
8. Toggle the battery main switch twice (Shift+M) This seems to work for me.
9. APU start.
10. Start engines (2, 3 & 1).
11. APU off.

This method has worked for me.
I don't bother with turning on the APU breaker as the engine start-up goes pretty quickly.
I'll do some more testing to try and find a way to use the various breakers.