Most virus dont make into a plants seeds, most virus used to modify genes are meant to be cured later on anyways, other virus are a bad choice. Mind that virus isnt the only means of genetic modification.
On the question: If the genetic modification does not cause failure to reproduce at all or even render an organism unable to live it can be bred out. Actually its way less likely for a population to preserve its exact genetic code at any moment than it is to change. This is valid disregarding the nature of the modification, by chance or intentionally, acording to a plan or at random...
So simply: Yes, any change in genes can be bred out if outnumbered by individuals not carrying it while not being highly preferable in terms of natural selection.
Now think of this scenario: A natural occurence of a species being widely outnumbered by GMOs that are not superior in terms of survival.