Unlike reality, Glass Flasks in Conan Exiles aren't supposed to be reusable most of the time, meaning that they will be lost upon use, forcing you to craft or find new ones. However, there are two exceptions: drinking all the water from Water-filled Glass Flasks until they're empty or mixing dyes with Dark or Light Dye Colorants at a Dyer's Bench will give you your Glass Flasks back. There are no current plans to change how this works, but keeping an eye out for future game updates is always a good idea since the developers are often prone to change old and recent content.