This also happened to me. Whatever theme I use, I always change the theme folder name in order to ‘white-label’ the theme and set it to something related to the site itself (as well as references to the new folder name within style.css). The folder name also changes as I add the version number on the end to know what version is installed. When I updated xstore before I didn’t have problems every time, but this time all the sidebars and widget areas disappeared or appeared in the wrong places. Something about updating from v3.8 to 3.8.1 was messed up. I don’t generally have problems with most other WordPress themes, but XStore seems to be problematic sometimes when updating. I think that your development team should take into account that some of us change the theme folder name from xstore to something we choose related to the site.
To fix this, I find that I have to “activate” the theme variant again, and then import my own saved options.json exported file to reinstate colour changes. I also have screenshots of where all the widget areas are supposed to be so I can move them back to the right position. Its a pain to do this every update to be honest. it shouldn’t have to be this way just because you have a different folder name or introduce versioning to the folder name.
Very likely, problem is related to renaming. Once you rename theme your site switch to default them. Next time, don’t rename old theme folder. Just open xstore folder with new version select all the files, them drog&drop files into your theme folder with overwriting http://prntscr.com/ef7kje
That’s all and you don’t need to rename old theme version, copy new folder, rename xstore theme folder. Just copy&replace files inside the folder.
Understood. What I don’t understand is why this problem happens with xstore and not all other themes though. I can name several WordPress themes that I don’t have this issue with. But from now on, I won’t include folder name changes for every version. Hopefully overwriting the contents as you mention will solve it.