I'm sorry to hear you're running into sync issues with WebDAV on eM Client. This involves an underlying issue in the eM Client, and they intend to release a fix in the near future.
In the meantime though, I would encourage you to redo the connection in eM Client. eM Client now offers a combined IMAP, WebDAV, and XMPP connection for SmarterMail users and it'll be the best IMAP / WebDAV experience for them. Please see these steps:
With that being said, you will want to leave the Windows WebDAV functionality disabled so that it doesn't override the SmarterMail DAV functionality. I hope that helps!
Kyle Kerst
IT Coordinator
SmarterTools Inc.
www.smartertools.com