Hey there
Don’t see how it could remove the changes as long as they were saved the css file remains the same as written. The Jat3 cache is found inside the plugins/ system/ jat3/ cache/ folder it doesn’t delete any of the css files in the template/css folders.
The only problem I have encountered with the jat3 cache cleaning system is it doesn’t always flush the cache, requiring a ftp look in the folder areas I described to flush. I could offer some suggestions, but not knowing your level of expertise, they might sound very basic common sense and annoying . 🙂
I can suggest you use a browser you normally don’t use to connect just to see what it shows, Sometimes it’s just a browser caching issue, FireFox is notorious for being a real pain to flush, I normally just use cccleaner on my system and it empties all the browser I have; cached files then I can see the changes. Hope it’s something as simple as the browser and you really haven’t lost all your hard work.
Blessings Shannon