Yesterday, as a reward for completing one of the Laurentian System missions- I received a Quantum Torpedo Mk III (+20 Critical) and equipped it on the ship, moving the Quantum Mk II to the aft torp slot and sending the photon torps into my inventory. When I logged on today, those items were all in place when I started the Patrol the Xarantine System mission. I did the Honad and Danteri missions and then on the way to Kern, somehow I entered Xarantine system instead (despite being at Kern) and suddenly I lost my Quantum III's- the QII was back in its front slot, and the photon in its rear slot.
This is the second time I've seen this behavior from the game, but the first time was with something minor and it happened around the time of a server crash.
You're apparently not the only one. My friend/groupmate just had his tier 3 escort rolled back to the last crash he had, so everything he got in between that and the crash.. which was quite a lot, is now GONE.