I want to add to this. It is possible for lifepods to switch off their location beacons. We have seen this before. When a TSN ship is destroyed, the life pods don’t always appear instantly. This is intentional so that enemy forces cannot locate and capture TSN officers. This doesn’t mean that this was the case however, but you can add it to the speculation when discussing in-character.
Another point… it could be possible to remotely program a ship. I know there are some who are not fans of this explanation but I don’t think it would be beyond the realms of possibility that TSN command could have been operating the research ship via a remote link, or perhaps have the ship pre-programmed on a set course with simple AI to respond to the dynamic situation should the need arise (just a basic AI though). If that is true, then what were their true intentions knowing a) the weapon would be so destructive and b) there were TSN officers aboard the escorting ships? Were we meant to return?
The disappearance of the TSN Destroyers we need to ignore. If it needs explaining in character, then we will have to settle for the classic “sensor glitch” or they hid their signals from us or something. Needless to say, it was a GM error and nothing more.