Window Sills are an integral part of the window. They are the foundation, the cornerstone, and when they become too far gone it is often inevitable that the window probably need to be replaced, but they can be revived if the rot has not gone all the way up the windows styles and backboards
However, this is usually only due to lack of maintenance over the years, as the majority of box framed counterbalanced windows were built with high-quality hardwood and it is amazing how long they have survived without maintenance.
Option 1
Lead flashing
When the sill only has surface rot it is adequate to flash the sills with a lead sheet, this old-school technique has been used for decades and can increase the life of a window sill for 30-40 plus years. The main purpose is to keep the sill weatherproof completed Restored Window Sill with Lead Flashing and draft seal.
Option 2
Replace sill with new Hardwood sill