The only dangers I see is that the original virus DNA might not be reliable removed, causing the (original!) virus to reproduce and attack the organism, or that the immune system identified the virus shell as dangerous, and starts an attack against the "infected" cells (which in the worst case might turn into a full-blown autoimmune disease).
The first part is actually pretty easy. You typically grow the virus using a plasmid construct you have created. That piece of DNA is just DNA without the viral mechanism, and you can easily sequence it to confirm you got what you wanted, as well as use various reporters for in vivo expression. When you express that plasmid in cells, the virus produced is only from your version and never came in contact with the original.
As for the second, I'm not sure why you would get an auto-immune disease from this - normal immune responses don't usually cause such diseases. In fact, that the immune system does attack and clear the virus (normal behavior), such that the virus is eventually cleared from the body. The goal is to have the gene inserted and expressed without persistent viral infection.