Any time you collect a probe card, mark that system by tapping it on the map and selecting "Probe" from the menu.
When you learn that the rebel base is not at a system by any method other than a probe card (gaining loyalty, subjugating a system, or via an intel mission), mark that system by tapping it on the map and selecting "Other" from the menu.
If the rebel player relocates the rebel base, open this help screen and tap the "Clear Non-Probe Marks" button, then re-mark any system in which you currently have loyalty or subjugation. Alternatively, just manually clear each system in which you do not currently have loyalty or subjugation.
If the rebel player plays the "Plant False Lead" mission, be sure to update the affected systems to "Other" status.