War isn't nice, so killing is expected.
Regular humans with practically the same DNA wage war all the time - whether over land, resources, or other property, it's been happening for thousands of years. There is no reason why two groups - especially of estranged species / different genetic makeup - wouldn't wage war even if they had a relationship years in the past.
You've also said the reptilians are "contemplat[ing] changing the status quo" and that the colonies are much more advanced. This can lead to a hundred different scenarios where they fight. To name a few:
- The reptilian civilization is angry about being left behind, so it attacks using the ships and nukes left behind on the surface pre-disaster. The groups fight over whether the decisions that caused the disaster in the first place were justified, and the hardships they caused.
- The spacefaring civilization realizes Earth is safe again after seeing the reptilians emerge from underground, but the reptilians want to use the Earth, too. They fight over territory and natural resources.
- The groups have completely skewed morals, and both think they themselves are right. Comparatively, the other people are savages, and must be eliminated for their crimes against god / nature.
- The reptilians want to be re-assimilated into human culture, recognizing their brethren and a better way of life, but the colonists refuse - which may include segregation, racism, slavery, or downright genocide. They revolt in an attempt to earn equality.
Notes on evolution
The "spark their reptilian DNA" part of the story not unheard of - some genes may lie dormant, and could potentially be expressed through a mutation. It would take a whole new question to work out the details, but it's not impossible for old reptile genes to be evolutionarily advantageous and thus spread across the population.
However, 200 years is a very short time to spread those changes! Evolution usually takes millions of years, and if everyone is isolated underground without connection to each other, there's no way to get the gene(s) to everyone in that time.
A possible solution might be genetic modification - publicly spreading advantageous genes to underground cities - but even then it's hard to connect the whole world, and you haven't specified exactly how people are living so this tech may not be available.
Additionally, The colonies on the Moon and Mars do not evolve sounds a little far-fetched. If the same amount of time passes, surely some changes will occur in both groups. Maybe the ones in space evolve more slowly - the population is larger, and technology has removed natural selection almost entirely - but they should still look and act different if the people on Earth do.