painting rotted sashes
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.