Meaning of "non-homologous virus"
It simply means a two dissimilar viruses. If you read the paper Falk and Bruening, they are worried that if you place a viral gene in a plant (here we call that the transgenic gene), then natural viruses may "mix" it's genes with the transgenic genes and create a superior virus. The thought is, you are speeding up the evolution of the virus by taking a beneficial gene from a non related (non homologous virus), something that would probably take a long time.