We just don't delete the original asset-files.
Think of them as the source files for graphics/audio/video. They get 'compiled' when you compile your project and the pipeline tool will see to it that it doesn't compile unnecessarily.
You wouldn't delete your main.cs file after compiling either.
But when you'd like to do the MGCB-stuff manually, just set the build-action of your MGCB-entry in the content folder to 'none'.
Here I have two pipelines in a single project. The first one, called 'Content.mgcb' runs automatically on build.
The second one doesn't, so I have to trigger it manually (or copy the xnb files to the output folder, or whatever. Depends on your MGCB project settings for output-folder).
Properties of 'Content.mgcb':
Properties of 'ContentAudio_Manual_3.5.1.mgcb':