Steps to reproduce the issue:
1. Add "build other projects (manual step)" in post-build actions to any job.
2. Apply changes, see this step is still activated after reloading page etc.
3. Reload Jenkins config from disk on Manage Jenkins screen.
4. See manual trigger action is missing.

Also, I noticed that job xml still contains step definition, but it cannot be loaded (because of data format inconsistency?).
Jenkins reports an error on Manage Old Data screen: "CannotResolveClassException: au.com.centrumsystems.hudson.plugin.buildpipeline.trigger.BuildPipelineTrigger"