This has been driving me insane since a recent Xara update.
I updated Xara Designer Pro+ and when I uploaded any web changes to Xara Hosting the file would corrupt and I would have to reload the backup.
I decided to experiment and completely deleted the older website on the hosting server which was uploaded using the previous version of Xara.
I uploaded the same website using the updated version of Xara and everything is working fine.
The file structure in the new version is completely different with a .htm file for every page.
That is something that you may come across.