I'm a returning player, and I've just started playing a new science officer.
In earlier missions, you have plenty of klingon encounters, and the groups of BoP's regularly cloak when they take a bit of damage and you get forced to fire on a different ship until they decloak. At least that was how I did it when leveling my tactical officer.
I've now earned the Sensor Scan ability and it's wonderful for decloaking these ships as soon as they go into hiding.
One problem: Why do these cloaked ships still have shields?
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They still go down even with the Advanced Battle Cloak anyway. I have a Lt. General flying the B'rel Retrofit and I can confirm that.