An error in one of our jobs produced:
18:58:34 ERROR: No tool found matching GRADLE_3_4_RC_2_HOME
Which leads me to believe that removing a tool from /configureTools/ you are unable to deselect it from the "Tool Environment" checkboxes in a job configbut it remains in the config.xml of the job, which can cause problems if the location no longer exists.

The fix is to remove the missing location from config.xml

    <hudson.plugins.toolenv.ToolEnvBuildWrapper plugin="toolenv@1.1">
      <vars>-GRADLE_3_4_RC_2_HOME,-GRADLE_4_3_HOME</vars>
    </hudson.plugins.toolenv.ToolEnvBuildWrapper>