(Ed note: Sorry about the delay. Hay fever hit hard and early this year and I was completely unprepared for it; it usually comes in April, not mid-March.)
The Voyager 2 probe spent an hour inside the stealth ship before being ejected. As the ship had matched course and speed with it, it continued on its way with no apparent changes. Unless someone happened to have been watching the entire process from start to finish, the disappearance wouldn’t even have been noticed.
Even for keen-eyed observers, if they noticed the disappearance it would seem like a sensor glitch on their side, as nothing about the venerable space probe had changed, at least outwardly. The only difference was that the insides of the probe had been swapped out for nanite colonies that took the shape of the components that were already there, but with the vastly increased capabilities of imperial tech.