This upgrade to BundleBuilder should not break your theme. That is also true for all of the customized code which was added for BundleBuilder in the past.
We do not expect this upgrade or any old customized code for BundleBuilder to have any negative impact on your theme or your store. We've been testing thoroughly for weeks now to ensure that.
However, Shopify is a very complex ecosystem with hundreds of themes, many of them heavily customized for reasons unrelated to BundleBuilder. The interaction between a merchant's store configuration and theme is always unique, and every app integration can also impact that functionality.
This makes it impossible for us to test for every possible scenario. Although we've done everything we can to avoid problems for our valued customers and we're very confident, we cannot promise perfection.