I have started randomly missing things from my ME. First a cobalt shovel, then two soul bound golden bags of holding, my logic processors and plate, my silicon chips and plate.. just random things. I also have smart cables running to essentia dispensers. There is at least one smart cable missing every time I log in. Ive gone through about 20 now. I play on Infinity Node 2.
My standard reply in this situation is : 1) Do you have an ME Security Terminal attached to your AE network? and 2) Break it, and only put it on when you need to re-synch your wireless - tho others have suggested that a blank AE Biometric card with Build permissions will also work. I've found that the security terminal is....often not quite correct in its assumptions, some times, especially if you've gone to another modpack, changed your title, or done anything that would alter your character data. The missing items are likely on an ME drive bay thats been disconnected by the agressive network integrity defense the security terminal employs - and popped off cables are another big point. Try it out for a bit and see.
Booker had me move the controller a block away and hook it together with a cable... and moved all my cabled things that kept popping off into the same chunk.. been ok since then. Unless I'm missing little stuff and just dont notice.
