(Another episode I'm reminded of is "Galaxy's Child.")

Well, according to Wikipedia: "Current methods of flare prediction are problematic, and there is no certain indication that an active region on the Sun will produce a flare. However, many properties of sunspots and active regions correlate with flaring. For example, magnetically complex regions (based on line-of-sight magnetic field) called [b][u]delta spots[/u][/b] produce the largest flares. A simple scheme of sunspot classification... is commonly used as a starting point for flare prediction. Predictions are usually stated in terms of probabilities for occurrence of flares... within 24 or 48 hours."

So there's some gauging method, if a broad one, though the stranded descendants might not have reinvented the technology yet to make a definite connection. Maybe the scientist I referred to earlier is pioneering the correlation between sunspots and flares?

If I may be a touch pedantic, we might prefer to call them "stellar flares" since they won't be coming from Sol, Earth's sun. I don't think a progression of flares would occur naturally, [i]but[/i] it could be manufactured. The entities that inhabit the sun's atmosphere or corona might, like us, be unable to travel in space unaided. In their case, they use ejected 'clouds' of ions, electrons and atoms - which are the very things flares emit. And if these entities are intelligent at all and have any sense of community, the ones 'back home' in the star's atmosphere may be trying to fabricate a 'bridge' or 'river' for their own wayward members to return by, the visible effect being an increase in flare activity. The difficulty for them might be in trying to recreate one strong enough to support a return trip, which has unfortunate side effects on the populace of the planet (in addition to the lost beings' behavior thereon).

The only way I see the flares being caused by the crashed ship is if it were some sort of research vessel that had been doing experiments on the star, triggered some reaction and were propelled onto the nearby planet. Whatever they did could have long-term consequences for the star, perhaps turning it unstable (artificially inducing its growth or collapse?), which puts them, the stellar beings and even the entire system at risk. Some initial (and probably hostile) encounter between the research team and the corona-dwelling beings might have eventually been translated into a mythical 'battle in the heavens' in the stranded group's religion, too.

As for the head scientist/commanding officer/what-have-you turned religious icon, I don't necessarily think they're still alive, since at least a few generations would need to have lived on the planet to forget most of their advancements and where they come from. But the leader's manipulation of the masses would be carried on through his church, perhaps led by a hereditary successor. That said, I'm unsure how a group of knowledgeable spacefaring folk could become members of a cult, but dire circumstances do crazy things to people and, if this is an alien species, they might have already had strong spiritual traditions that survived into their society's warp-capable stage of advancement. But the stranded people could either be a theocracy with a (re)burgeoning scientific underground, or the church might simply be an influential but not dominant facet of the newly arisen culture.

As for the entities on the planet's surface, they needn't have been there for as long as the people, though that's possible. It could support stories of 'demonic' encounters or something, though their proximity would need to be fairly infrequent if this illness is considered unusual by the populace. I imagine the beings are semi-solid or gaseous and plasma-based, largely invisible to the naked eye except for perhaps a vague shimmering outline, like in [i][url=http://image.tmdb.org/t/p/original/rHzVbibGGycUelThXx0swbSuyez.jpg]Forbidden Planet[/url][/i] if you've seen it, or such as appears over blacktop on a hot day. In terms of shape and ambulation, they might mimic the helical, serpentine look of "[url=https://en.wikipedia.org/wiki/File:AR1520_and_Shimmering_Coronal_Loops.ogv]coronal[/url] [url=https://en.wikipedia.org/wiki/Coronal_loop#/media/File:Traceimage.jpg]loops[/url]" or perhaps something  in the vein of very bizarre deep-sea organisms. They might be angels or demons to the religious folk and could be called things like "sun dogs" (actually an earthly phenomenon, but still a neat term), serpents/snakes, dragons, worms, or otherwise, depending on what we model them after.

Oh, and some more [url=https://www.youtube.com/user/gazorra/videos]TNG lulz[/url]. ;)