Honestly dude? It's just guffin McGuffin stuff from sci fi that serves the purpose of a game mechanic. If you want lore, yes, ask a lore thread.
If you want something relatable to modern science?
Flux: Most likely the ship transferring heat internally to "flux capacitors" from the ship firing weapons, using special systems, using shields etc. Heat is one of the lesser known but crucial aspects of building any spacecraft, it may be near absolute zero outside in the vacuum of space but there is almost nothing to take it away.
You may have recently heard about the international space station had a problem with one of the heat pumps - they had to turn off almost all non-essential electrical systems and suspend experiments, else the inside of the ISS overheat causing malfunctions and killing the crew. You know those big white "Solar Panel" looking things on the ISS? They're not for taking in light to make electricity, but to are pointed away from the sun so as to radiate heat away from the craft.
So anyway, when you vent flux the McGuffin "Flux Capacitors" are probably venting the ship's built up heat through heated ionised gas or radiated in a spectrum that is visible to the human eye.
Shields: There are many theoretical shields that are discussed since their advent in shows like Star Trek, some speculate you can use high intensity magnetic fields to deflect ionised particles, however there is no known science surrounding the projection of a field that can deflect non-magnetic materials or laser beams*. *You can deflect lasers of course with a simple mirror, but a mirror surface would eventually overheat and melt.
That said there are theories about using exotic matter to create negative energy fields to manipulate space/time to move a ship through space. If you can do something that complex you can probably manipulate space in such a way to simply divert the incoming light/penetrator/missile somewhere else. Said manipulation of space time would also allow you to destroy physical objects by stretching or compacting space/time so much that the object's chemical or strong force bonds are overcome.
In theory.
