SharePoint Designer uses caching which can overwrite your changes. I have done this MANY times.
1. Best way to avoid this is to turn off caching for Designer but your site may run slower.
In SPD go to file > options > application options – second to the last checkbox “Cache Site Data across SharePoint Designer sessions”
2. Each time you open your CSS file make sure you hit the refresh button in the top right corner to load the latest not cached version.
If you need I will find the instructions to for turning of site caching so you dont have this issue in the future. I have turned it back on as the site was inreadibly slow and am very aware that changes can be overwritten if I dont hit that refresh button.