So TS is fine, The TE is the affected toon. TE basically had the ship configuration and vault of my TS mapped over.
I believe the reason for this was because the account slots that I was moving around, I had moved the TE to where the TS was just before that.
As to everything I lost, I know I had the following:
Smiter's Wrath, Sting of the Mordana, Black Caster, Prototype Dark Matter Launcher, Ya Zi Long's Hellbore, 5 Zets, Ego Matrix, Intolerance, Plague's Bite, Bully Eye, Aegis of the Warder, CVE, Biomechanical Langour, Sai Li's Circle, and Intent and Viper Engines are all of the major things I lost. There are also a ton of ammo comps I was hauling as well because my TE is my primary ammo builder. Some of the things my TS also had, but my TE had everything at a higher percentage of quality.
As for how long they were offline... I'm not sure. I'd definitely like to try a couple of things out to see if there's a potential exploit people could use.... because things like this cause a reverse-exploit... like instead of getting things copied, you lose everything, lol...