Subversion Update Project removes most file from working copy

I'm using Subversion with build 5289, and I've just done Update Project. It removed most of the files from my working copy!
Has anyone else seen this?
I've seen it twice - on a working copy which wasn't fully up-to-date with the repository, and on a fully-updated working copy.

I done an update from Tortoise, and it works fine.

.

Thanks,
Calum