When I first created our website, I did so by creating a theme override based on an existing WA theme. When I tried to update my theme, I broke the website, apparently because WA had meanwhile changed things behind the scenes that were no longer compatible with some of my code in the original theme. Presumably the needed changes had been automatically made to my existing theme but were overwritten when I uploaded my changes.
It would save a lot of grief if a theme could be selectively modified by uploading specific files, instead of an entire theme.
It would also help if WA would provide some sort of merge facility. Ideally it would:
1. provide timestamps of the existing files and those to be replaced
2. highlight the differences between existing theme files and there replacements
3. provide versioning to allow web designers to recover from misconfiguration without having to call on WA support.