Not only .uvs dir has to be empty for fresh restart, but uppsrc as well.
Or, even better, just try with different set of dirs.
uvs2 would not remove existing files.
And yes, there is always complete history in local archive, included all deleted files.
Sorry for inconvenience, something strange happening here. I have checked myself (by syncing to empty archive/dir), Daniel does not have those deleted files in Core too. I really would like to know what is going on here.