You're probably thinking there's a smooth path from the deprecated SuiteBundle functionality to the SDF functionality promoted by the deprecation banner on the SuiteBundler. Nope, there isn't.
First, if you exported your bundle as an SDF project, be aware that the exporter creates an Account Customization SDF project. There is no uninstall path for an account customization project, so you do not want to use that for 100+ clients.
So you will want to create a SuiteApp SDF project and pull your resources into that. There isn't an automatic exporter for that even though it's the closer match to a SuiteBundle.
Then, when you try to deploy your SuiteApp SDF project to an account with the existing bundle, every single resource will be treated as a duplication error.
The only advice we've gotten from NetSuite is to turn our new SDF project back into a SuiteBundle that can be deployed over the old bundle (in our case the SDF project is a reimplementation with significant overlap of the previous bundle, not just a repackaging).