Running Jenkins 2.121.3 on Windows with Apache Tomcat, I've configured JENKINS_HOME in the default location in the C drive under a user's profile. However, due to hosting a large number of projects, the workspace and builds directory are stored in a separate drive, configured in config.xml, i.e., 

<workspaceDir>E:\workspace\${ITEM_FULL_NAME}</workspaceDir><buildsDir>E:\jobs\${ITEM_FULL_NAME}</buildsDir>

ThinBackup 1.9 provides options to "Backup Build Results" and "Backup Build Archive." This does not succeed in capturing the data stored in the configured buildsDir. The backup file contains only the config.xml, disk-usage.xml, and nextBuildNumber, mirroring the contents of the jobs folder under JENKINS_HOME, but not any of the numbered build folders and associated artifacts which can be found in the buildsDir location from the data drive.

I believe we can work around this by manually saving the contents of the builds directory on our data drive, but it presents a potential problem for restoring successfully from a backup if it's out of sync with the ThinBackup file set.