Just completed the "Perform Scan Overlay Analysis" task of the Xathe Vortex legion mission. That means that I had to scan a lot of planets in order to find 20 of them that were blue gas planets. Scanning all those planets lowered my scan chance rating, which is what I expected. But now I can't get my scan chance rating back up. I upgraded my scanners to Continuum Analyzer Mark III, and I purged a lot of planets, so now I have fewer planets in my scan than I had before starting the mission. So with the upgraded scanners and fewer planets in my scan base, why is my scan rating still poor? (My scan is 10167 before buffing, and I have 667 planets in my scan (189 owned, 5 legion owned, 113 enemy owned and 360 vacant).

Click scan once. Sometimes it doesn't update the "Planets Scanned" until you do so.

Also, were you running buffs the first time that you didn't replace the second time?