Wood rotted on thermal pane windows
First of all treat the rot with an appropriate fungicide.  You do NOT want one that coats, but rather penetrates.  

Look for WEST -- wet epoxy saturation technology, or something like that.  

In a nutshell:

Remove the clearly rotten wood.  Initially mix up small batches and paint it on.  If you find it leaking through use some fine mesh fiberglass cloth to seal it.

If the holes are large, wet blobs of fiberglass chop, and stuff in there. Paint the entire surface with the resin to seal it.  

You can mix colourants into the resin. Since paint doesn't stick well, decide on a colour for the final coat or two.

It's been 25 years since I've read about this.  Details fade, and practices change.  But if the wood is only starting to rot, you may not need to replace it.