If a player's species starts with a vulnerability to an elemental damage, or light blindness. What happens if the character is able to overcome that detriment. Do they "return the ability bought" with that negative like how Drow lose half their darkvision & spells?
There is no general rule that requires a character who overcomes some sort of racial disadvantage (by feats or otherwise) to consequently lose some other racial advantage instead. The character has already paid some kind of cost - such as using one of their limited feat selections - and the game does not punish them for doing so by taking away some other feature. If we were talking about a species with a racial penalty to Strength but a bonus to Intelligence, and the character chose to improve their strength when they levelled up, would you say "working out made your brain shrink, lose your +2 Intelligence bonus"?
The rules also do not offer any kind of association between a species' different racial traits to indicate a particular advantage has been "bought" by a corresponding disadvantage.
Resistance does not override vulnerability anyway
In the specific example of a character who has both vulnerability and resistance to a kind of damage, these two mechanics do not directly cancel each other out as they work differently. Vulnerability means the creature takes an extra 50% damage; resistance subtracts a flat number from incoming damage. These both apply at the same time; being resistant does not prevent one from also being vulnerable.
So, for instance, a creature who has sonic resistance 5, sonic vulnerability and takes 20 sonic damage takes a total of 25 damage; the incoming damage is increased by 50% to 30 because of their vulnerability and then reduced by 5 because of their resistance. They clearly haven't completely overcome their vulnerability to sonic damage, because despite their resistance they've still taken more damage than a creature who wasn't vulnerable would.
(I have assumed that vulnerability applies before resistance as Starfinder is not clear about how exactly these rules interact, but this is the order of operations that seems established in parent system Pathfinder, as per this question. It also doesn't change the argument if it were applied the other way around - the specific value of damage taken may vary, but it's still more than a non-vulnerable creature would normally take).