I'm guessing it was either a site, CDN or browser cache issue, unrelated to the plugin. If you are using W3TC or any other page cache engine, make sure to empty the page cache and update the query string and reload the page with CTRL+F5 to empty the browser cache as well.
The search instance dynamic CSS is generated to 1 file for much better performance. If the browser caches too aggresively the changes might not appear after saving at first refresh. Webkit browsers like chrome or safari have crazy strong cache engine on CSS files, so I usually refresh with CTRL+F5 multiple times just in case.Best,
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