From "The Immunity Syndrome" -
Interesting. No indications of magnetic storms in this sector.
Ships disappear all the time in Star Trek. Even when there are records of the ship in the LCARS, the crew of a starship might not know about the ship or its mission. I have seen episodes where this has happened, "The Royale" and "The Sound of Her Voice".
True, ion storms - a type of magnetic storm - can move at warp speeds. Can they move a vehicle twenty thousand light years to the galactic barrier? That is the distance from the barrier to the Federation, unless the barrier is closer. (The Nth Degree has the Federation approximately thirty thousand light years from a point near the galactic core.) Then, how close is the barrier? The best that I am able to determine is that ion storms can go from one sector to another, before fading out.