We're using a local installation of WebProtégé 3.0.0.
When trying to upload updates to our ontology, we get the error "An error has occurred. Please try again. null". Then, just after applying the upload, the updates appear to be there anyway, even after a couple of "refresh tree". But when coming back after 5 minutes, all the updates coming from the upload are gone. This makes me think that the error when uploading matters.
Is it a known issue? Let me know if you need the data to reproduce the issue.