The scheme is the following. There exists a package called foo (an API under heavy development, in first alpha phases) whose rst files are auto generated with sphinx-apidoc.
For the sake of having a better documentation for foo after those files are generated, there is some editing. In, say, foo.bar.rst there are some paragraphs added to the contents generated with sphinx-apidoc
How can I not loose all that information when a new call of sphinx-apidoc is made? And of course I want potential changes in the API to be reflected, with that manual information added being preserved.
sphinx-apidoc only needs to be re-run when the module structure of your project changes.  If adding, removing, and renaming modules is an uncommon occurrence for you, it may be easiest to just place the rst files under version control and update them by hand.  Adding or removing a module only requires changing a few lines of rst, so you don't even need to use sphinx-apidoc once you've run it once.
Keeping the API updated in Sphinx