I'm not sure why you're having this issue, as I can see them (green (right) and red (left)) when I'm using either the External Power, or the APU with the APU Gens ON, or the engines running with Gen 1 & Gen 2 ON. Whether the Anti Collision lights are ON or OFF makes no difference, I still see them.

Have you downloaded and installed the 1802 update?
If not, then you can get it here: https://captainsim.com/products/x737/sp1800.html (make sure you download the Prepar3D 2/3 version).

The update not solving the problem:
Have you tried a complete reinstall?
Have you checked to make sure that after turning your AV back on that it hasn't removed a file it has flagged as a false positive?

Something that I always do is this. I add the location of the Captain Sim installion files (F:\Captain Sim Products), and the location of the Prepar3D v3 installation (E:\Flight Sims\Prepar3D v3) to my Anti Virus Exclusions list.