Well, sharing 3000 files is approaching limits. The reload task is done in the foreground and takes a while. Amulecmd uses synchronous communication which times out in this case. Some other things might break too (like connections can timeout). You did compile amuled with optimizations?
Moving the reload to a background thread might result in a lot of new and interesting problems, but would be the best solution.
But maybe a little tweak to the reload code might do the trick. I don't know what exactly takes so long, but I sure don't like that linear search in the known file list.
