I've had the same thing happen to me, only it was never confirmed that I did throw my emp (it was however the most likely option). The SGM told me they could not restore it because it "interferes with quest progression" and that nothing from Trial of Magians can be restored. This part definatly needs to change, since it means that Relic and Mythic Weapons are now exempt from the one time restore as well.
I'll ask SE again, and I posted this last year when it happened: What's the point in a one time restore when the most difficult to obtain weapons (looking at Mythics), and other time-consuming weapons are exempt from it?
Luckily I did redo my Emp, so all is well now.