How to replace the old Feature Framework with remote provisioning

We have a large scale document management system with multiple site collections (record centers), each with about the same 80 content types + fields.

They are currently deployed using the old feature framework. We want to replace this with a remote provisioning strategy.

What is the recommended way of removing features from an existing environment? I know that SharePoint would complain about missing features in content databases.

Guess we need to run some scripts to clean up existing content databases?