I have this problem with Applied Energistics completely resetting. It still has items but none of the blocks are connected to each other. Here is a picture: As you can see the cable has disconnected and the ME system is no longer online.
This is a known bug, and unfortunately will not be fixed until we update to 1.6 (if we ever do). Replace the controller to temporarily fix this.
Problem is I have to replace EVERY SINGLE ME block. Sometimes it is fixed with a relog, but sometimes it doesn't
This is a known issue for which there is no available fix since AE is no longer being updated for Minecraft/Forge 1.5. The issue appears to be resolved in the newer versions of AE for 1.6.4 which is currently undergoing testing. In my personal experience, when this happens, I have been able to just break and replace the ME Controller block to get the core machines going. However, my ME system has not had the cables glitch up like shown in the screenshot.