git-annex-export currently only copies git-annexed files to the target remote, omitting files under normal git control. So for the target to fully reflect the exported treeish, all files in the treeish must be git-annexed. It would help if there was an option to export git-controlled files along with the git-annexed ones. This is useful e.g. if you have a version-controlled website, and want to version the basic html skeleton with normal git, while versioning heavy data files with git-annex.

done notabug --Joey