Do you allow it? If so, what mechanics are involved, if any?

I would allow it sure, but it would be it's own campaign goal. Like, an entire campaign. The PC's would have to do tons of exploring and researching to even learn about what vergences are, how they function, and if it's even theoretically possible to alter them.

I would require some kind of force rolls while they are there, trying to purge the place. Possibly using something like Suppress (shutting down the current "flavor" of the vergence,) so another can take it's place. Require them to only use Force pips of the color associated to how they want to change the vergence. For example, you can't use dark side pips to power your Force powers, if you are trying to purge a vergence of dark side influence. Etc etc.

I'd probably create some artifact that helps to alter the flow of Force energies in an area, to provide assistance on the rolls, something like that.

Do you allow it? If so, what mechanics are involved, if any?

It would depend, and if allowed it would NOT be an easy thing to accomplish.

Most vergences are incredibly ancient, measuring hundreds if not thousands or tens of thousands of years old. It's going to take a LOT of work on the PCs part if they want to change a dark side vergence that's been around for several thousand years to be a light side vergence.

In the case of Mountaintop Rescue (the Beginner Box adventure), the region has only very recently been "polluted" by the dark side, so the PCs will have a much easier time "fixing" things, especially as the grounds surrounding the temple are not a vergence.

As KungFuFerret suggested, changing the nature of a vergence (if even possible in the first place) would be the major focus of a campaign, and not something simply hand-waved with a few skill checks. The PCs would probably have to do a lot of investigation and research to see why a vergence has the particular nature it does, and even then it may not be possible for them to change its nature, as sometimes the Force just simply "is" with regards to certain things Even Qui-Gon's mention of midi-chlorians indicated that they were at best a measuring tool, and offered zero insight into why a person was sensitive to the Force. Anakin's two kids were both born strong in the Force, but that's not to say that every Force user is going to have offspring that would be sensitive to the Force, as I'm sure there are cases where two Force-sensitive parents have a child who isn't Force-sensitive.

All good advice! I asked because the PCs in my campaign found a weak vergence aligned to the dark side. In it's past it was neutral, but years of the temple being held by a tyrant as well as holding a Force user prisoner, tainted it. That's probably not how they work, officially, but it's what I did.

I'd like the PCs to be able to use the vergence map they found there to gain more lore, and I think cleansing a vergence will be a great reward, eventually.

All good advice! I asked because the PCs in my campaign found a weak vergence aligned to the dark side. In it's past it was neutral, but years of the temple being held by a tyrant as well as holding a Force user prisoner, tainted it. That's probably not how they work, officially, but it's what I did.

I'd like the PCs to be able to use the vergence map they found there to gain more lore, and I think cleansing a vergence will be a great reward, eventually.

If it's only been a few years, or even just a few decades, then I'd say shifting the place back to neutral (or maybe even light-aligned) should certainly be possible. Of course, keeping it light-aligned (if that's how the PCs opt to go) is going to be a major undertaking as well.

But again, I wouldn't make this an easy thing that's resolved and done as a single adventure.

The beginner's box add-on adventure "Lure of the Lost" you actually go through the process of encountering a vergence and it includes rules for "cleansing" said vergence from the dark back to the light.