The flickering you see only manifests when the cinematic sequence is rendered out into an image sequence. It does not happen when previewing the same sequence in the viewport. I’ve isolated the issue to the cast dynamic shadow option on the rect light casting the light that flickers.
However, I am perplexed as to why that specific rect light is having issues while all the other rect lights casting the blue glow you see on to the underside of the ship do not cause this flickering. I also find it rather strange that this only happens when the cinematic is rendered out.