Okay, just found the solution (for me and perhaps other PC users, anyway). Apparently ED-E was somehow disabled, which was why moving to him or moving him didn't do anything. Simply type the following in the console.
prid 1732D1enable (you may not need this if he simply got stuck somewhere)moveto player
Unfortunately using the console (for anything?) seems to disable Steam achievements...so if you care you'll probably have to reload an earlier save. Or perhaps a quick mod could be made to replicate those console commands?
Edit: He disappeared again hours later. :brokencomputer:
(Oh, and if you've completed ED-E's quest, you may need to use one of two different IDs (1732D0 for the armor path, 1732D1 for the weapon path).)