According to the plugin wiki (https://wiki.jenkins-ci.org/display/JENKINS/Multi-Branch+Project+Plugin):

Sub-projects appear to be configurable, but they will be overwritten by branch indexing if you manually modify them.

But after I made changes to sub-branch project and run branch-indexing,
the sub-branch project configuration is not overwritten,
and further changes from Multi-branch configuration is not sync over to sub-branch project anymore.

Symptom:

You will see Detected unsupported subitem f.q.ClassName@hash[my-multibranch-project/my-branch], skipping in the indexing log.