Assuming that the Mobile HPG is working, that is it wasn't affected by the virus, the only reason it won't work in places would be the theory that the virus caused the HPG's it affected to somehow alter local space-time to prevent transmissions must be true.
As far as I'm aware, it's been established that it's the medium that kills HPGs (in
addition to sabotage, attacks, and apparently a virus/malware). In
A Bonfire of Worlds, a completely new HPG built from all-new components from all-new factories, that never received any transmission, still burned out. It couldn't have been affected by a virus and it wasn't attacked.
The "Clarion Note" protocol that was enacted by means of a SHPG supposedly altered the hyperspace medium in a way that wrecked the HPG cores of older HPGs. It was said (in
Ghost War, iirc) that it was the newer stations that were attacked to bring them down.
So the theory behind what's happening should be known - newer HPGs are shielded against the Clarion Note effect, so somebody saw a neccessity for a design change somewhere, for some reason, back during the Star League days when these HPGs were all built.
There's a fan theory that Clarion Note and Fortress Republic, two edge case KF physics protocols that happened to overlap, somehow interact(ed) in unforeseen ways, exacerbating the HPG problem.
Stan Gibilisco's Understanding Einstein's Theories discusses hyperspace communications.
What SCC said. You're working off a misconception here.
BattleTech's Kearny-Fuchida "hyperspace" is a purely fictional and poorly defined thing; but we do know that it doesn't exist as a space to move through. Jumps are effectively teleportation, without moving through any space in-between. And HPGs simply teleport electromagnetic waves. No dishes, antennae, or beams that could be focused are involved in sending out a HPG message.