I am trying to fix discolored and rotting lower sashes on my natural pine windows. The wood has turned green. I am using a wood petrifier to firm up the wood. How do I paint/varnish that lower sash to match the rest of the natural lightly yellowed pine sash once the petrifying is done?
If you want to keep a natural/varnished finish, you'll probably need to replace the rotten sash. Which is also the correct solution to a rotten sash, really.
You can try bleaching the repaired area, but I doubt it will work for the level of "work" required to look good as a plain/varnished item.
As such, either paint both upper and lower sash some solid color (or just the whole lower sash could work, if wood above/paint below suits, and that leaves the option of going back to a full natural/varnished look when you do replace the lower sash) or replace the rotten sash with new wood. You'll also need to address the reason the sash rotted in the first place.
If you are a cheap and/or lazy person like me, the wood "petrifier" is a good idea and then use a clear wood stain - you could try to find a stain that will match at home depot, but I doubt you'll get a perfect match. Note, you really can't match the existing pine perfectly, but in time they will start to look the same.
This is not how a professional would do it - they'd replace the entire window, revealing further rotting, leading to a demo on the interior and exterior walls, leading to a new house.