I am starting to work on a fork of the editor and wanted to stay up to date with threejs releases. My question is what is the best method or pipeline to do this?
In general it can be very difficult to upgrade code if you are forking software.
The migration guide is helpful when you just upgrade the library for your app. In your case you normally have to merge the contents from the release commit to your forked branch. Depending on how you modify the editor, this can result in heavy merge conflicts.
If you only add small changes to the code base, you should consider to add them from scratch to the latest version of the editor.