There are times when ODK Central itself will set the version string, generating its own XForm. This happens when publishing a Draft Form whose version string conflicts with another version. It also happens when using Project Managed Encryption. This process can lead to Central not saving the XLSForm. However, in Central v1.3, we made a change so that the XLSForm is saved when a Draft is published even when Central sets the version string.
We still need to do something similar for Forms that use Managed Encryption. I think I'm seeing that when Managed Encryption is in use, the XLSForm is never saved, not just when encryption is first enabled for the Project. There's an issue filed for this on GitHub, and I've updated that issue and added a link to this discussion.