It feels like you are describing two problems
Running 3.67.1 with java.endorsed.dirs=lib/endorsed argument requires java 11
Commenting that line out to get the application to start means you are using java version 8 to run the application.
We ship two different binaries depending on the Java version you intend to use.
If all your repos are present, but empty, it means the database has configuration data at least.
Now you need to define "empty".
Do builds fail to download anything?
Is the browse view Empty?
Do search views or searching return no results?
There are tasks to rebuild browse and search.
if you can't download any content directly, it suggests there could be problems accessing blobstore content. In that case, check the nexus.log for ERROR or WARN messages when requesting content.