Does C of O for combo unit lower taxes?

Can't speak to BPC. But whether you get a new C of O or not, your % ownership of the building remains unchanged.

Right. The city just adds the percentages of common interest.

Take http://streeteasy.com/nyc/sale/599579-condo-45-w-67th-st-lincoln-square-new-york, an A, B and C combo where the tax lots weren't merged until December 2010. In 2010 the total assessed value for the three lots was $299,156, while the 2012 assessed value for the merged lot is $323,586.

Forgot to say, that 8.17% increase was the same as for 15D next door.

Note that real estate tax is computed for the building, not the individual units. Unless you're talking about a building that's going from 4 units to 3 or something that triggers a tax class change.