Every now and again and usually after a crash, when I start up AE I get a message saying that the AE media cache folder does not exist. When I check on my drive for that folder, AE is quite right - it is not there. I use a seperate SSD for all my media caching and another drive for footage and another as my strartup drive. I set AE to use a folder called A:\AE Cache. For whatever reason AE is deleting this folder. Other folders on this drive remain as they are. Unless I have a goblin sneaking into my suite on a night deleting this folder or Windows decides to delete this folder all on it's own then it is almost definitely AE that is doing it.
Traditionally A and B are reserved for removable drives on Windows - they used to be the old boot drives for floppys. It may in fact be Windows doing something odd. Try to assign a different drive letter.
The media cache is shared with other Adobe applications, including Premiere Pro. Are you doing something in another application that might be affecting the cache location?