Renaming a job causes a commit to be added to the scm-sync plug-in's internal commit queue (see ScmSyncConfigurationBusiness.java) that fails due to the issue documented in JENKINS-15128 - Renaming job doesn't work with Git. Thereafter, even if one cleans up the checkoutConfiguration directory and manually syncs everything up, it become necessary to restart Jenkins because the failed commit poisons the queue. The remaining issue with 15128 (not calling git rm with the recursive flag) means the commit can never succeed. All subsequent configuration changes get stuck behind it.
There needs to be a way to reset the queue queue w/o restarting Jenkins.