Comment 1 for bug 1395459

After doing a bit of searching, there is a patch in upstream berkshelf already, which will fix this issue:

https://github.com/berkshelf/berkshelf/commit/75525092a20a3194795577e1e277299d90f0a056

This will cause "berks vendor" to sync an existing cookbook directory instead of insisting to install into an empty directory.