If you do change the file, and that file loads into browser (which it clearly must do), and modified properties don't apply, this means the old file is cached. X3 actually has a built-in workaround for this, but it does require you to click "save" in panel, so that it clears the actual X3 page cache. In this case, it will then append a date behind the file request "?MODIFIEDTIME".
even after clearing the cache.
What cache are you clearing though? The CSS would be stored in your browser cache (X3 itself can't/doesn't cache any CSS). And even if you clear your browser cache, depending on your server, the request itself could be cached on a proxy (like Cloudflare, if you are using that).
Please click "save" from panel, every time you edit/upload a modified CSS file. This should work. Otherwise, you would need to send me exact details and links to the CSS files, and tell me what classes are not applying.