I have been separated for 20 years. The separation agreement was signed in Guelph, On. Do I have to file with the courts in Guelph or can I file here in Owen Sound?

You will have to sign where the separation papers were initiated, Guelph.

You might check with the courts. Many courts if the matter isn't moved on in a certain number of years (depending on court rules) then it is set aside. You may have to start everything all over.