The lower edge of the center window of a bay window has begun to rot away. There is no indication of a leak from the outside so the assumption is that condensation on the inside has caused the wood to rot. According to Pella help desk the entire bay would need to be replaced. Center window cannot be removed separately. The cost of doing this is prohibitive at this time so I would like to do a temporary fix by filling in the rotted area and repainting it to match the rest of the trim. My question is what is the best filler (Putty, Epoxy, etc. ) to fill the edge. (see photo)

I would only use an epoxy filler. Read this link How to Use Epoxy on Wood for Repairs | The Family Handyman (http://www.familyhandyman.com/DIY-Projects/Home-Repair/Exterior-Repairs/Other-Exterior-Repairs/how-to-use-epoxy-on-wood-for-repairs)

I have replaced many center windows separately. You can use a fixed sash, painted to match.