Found an answer on the Oracle Commerce Communities (need to log in).
Unfortunately, the thesaurus is no longer able to be maintained via the pipeline XML and emgr_update settings in 3.1 Tools And Frameworks, since it is now managed within the content repository. The only supported mechanism for importing/exporting the repository contents is via the application's import_site and export_site scripts, or editing entries directly in Workbench itself.
In the next version the configuration is going back to being more file-based instead of only accessible within the repository, so the files that contain thesaurus and rules, etc, should become easier to manage if you preferred the older architecture of XML config.