It probably wont show its effects until much later.
It seems rather unlikely, though.
Especially regarding that much more genes change in artificial selection, so - from a gene standpoint of view - I would assume that the more genes change, the bigger the risk by that logic. ;)
I can tell you that a healthy dose of skepticism never hurt. Uninformed fear, however, is an utter nuisance.
Though, I totally agree with you here.
It's not that it's unlikely. It's that we don't know and probably will never live long enough to see the effects as the selected genes interact and evolve with the original species.
Eukaryotic gene interactions are a lot more complex than what can be observed in prokaryotes. Take humans, for example, we have so many products from ~20K genes. It's not as simple as transcribe a segment, translate it, and boom product.