This warning often appears in the References tab:

This warning appears if your server has references listed in the Obsolete References section. Your action in response to this warning depends on your particular upgrade scenario and obsolete references situation:

• If you upgrade from release 2.2 or higher to 4.x, you do not need to rebuild your reference indices.

• If you upgrade from a release earlier than 2.2, you must rebuild your reference indices after the first upgrade to a 3.x or 4.x release (and before using the upgraded server for analyses).