Do you use Child themes? I don’t know if it may be the case, but when you use the parent theme, whenever you have an update, you can loose all the customization you set before. We have to always make a child theme. There is the “Child Themify” plugin. I don’t know if it is your case…
I always used Twenty Eleven I have never had any issue until now . It has been several years. Its only been recently that I had this issue. It doesn’t matter what version I put or what theme I use it loses all format. Like running the website without JavaScript. I could be transferring a virus from my computer with thumb drives trying to solve issue. I know for a fact one of my computers has a virus. I just reset back computer a year hoping I get rid of this virus. The computer is a windows 7 and I have Bitdefender which is not showing any problems. But performance using browser is slow. Usually I can tell when I have a virus. The problem always happens when I save under Setting. I am trying to put url where it says http://localhost and set it to http://smallprogramdesign.com like I always did. Everything is functional but the Setting as soon as I save I loss formatting. I taught it was windows 10 but my Windows 7 does the same thing. Some where along all the updates or theme changes something is not functioning right. I know the newest Plugin and only plugin I have is Akismet in this fresh install. My next step is to try my Windows 7 computer again now that I rest it back a year.
I see… unfortunately I have no idea what to do in this case. Sorry about that. I hope you can solve your issue as soon as possible.