Your issue isn't clear (at least to me), you can update Publish Online documents by using the Update Existing Document facility – do you mean instead, you want to be able have the InDesign document linked so that it automatically updates the Publish Online document when you make changes to the original?
It is not possible to publish an *.indb online. You can only publish *.indd files. It would be great to be able to publish indb files that are updated automatically as the associated indd files are updated.
are you publishing books online and using publish online as your platform?
the publish online feature is not a service meant for "real" world use/commercially. if that service is gone tomorrow you will loose all of those files.
you should really consider a platform that would not go away tomorrow if adobe decides to scrap it. its a free service and it can go away anytime.
Just don't want you to be pulling your hair later if this all goes away...