I am able to patch system module files using these instructions. https://openjdk.java.net/projects/jigsaw/quick-start#xoverride
When trying the same command to patch a package-info.java, the package-info.class file is not generated if the patched version has the same contents as the version in the module. But this behavior does not apply to non-package-info java files.
javac --patch-module java.base=src -d mypatches/java.base \ src/java.base/java/util/concurrent/package-info.java
In my original question I mentioned the following error:
package-info.java:2: error: package exists in another module: java.base
I am still trying to create a toy example to reproduce this error. The main difference is that I am using a custom system module (--system) when I get this error.