I had similar problems when I first got my MC200 I had a largish FLAC library for my Squeezebox system and naively tried to drag and drop the whole thing. It did what you've described and left a bit of a mess not really knowing what had imported and what hadn't. In the end I imported artist by artist and even then it would just decide to reset itself every now and then. It wasn't quite so smooth as I'd hoped! In the end I quickly filled the MC200 and bit the bullet to get an MD600 with various end points. I ended up having to repeat the import artist by artist as I decided this was the best way to ensure everything from the squeeze-server was imported. The MD600 seemed a lot more stable than the MC200 during the import process but you could still "overwhelm" it if you tried and get the thing resetting itself. (I say seemed, of course I was a bit wiser by then and treated it much more gently!)
This was a wired connection. it was a bit annoying to have to hand-hold the import quite so actively but it gave me the push to do some tidying up of the metadata as I went, especially the second time round when you've discovered a few foibles but they weren't quite annoying enough to stop listening and get them sorted after the first import!
Good luck with it, it is worth it!
Main system; G68ADV, G98DH, MS600, HD621, DSP5.2KC, fronts DSP5.2K, rears DSP5K, D1500, various sources, 60" Plasma.
Second system G68ADV, G98DH, MS600, HD621, 2x DSP5K, DSP5KC, various sources, 55” LED.
MD600 tucked away in study. Lots of other Meridian!