Will my bundles still exist if I uninstall and reinstall Bundle Builder?

Your bundles should remain in place after uninstallation. When Bundle Builder has been uninstalled, existing bundle products won't work and may need to be hidden from relevant sales channels.

 

Therefore, when Bundle Builder is reactivated, everything should link back up. Bundles that are in place would just need to be made available for sale again from within the Shopify admin space.