I am also having trouble deleting old tracks, waypoints and addresses that are only showing up in BaseCamp. I have deleted all my GPX files on my devices, Zumo 590 and Nav VI. But when I plug it in and have BaseCamp open, it shows my internal storage close to being completely full, I only have the one map on it, and there is stuff from years ago which I want deleted. I keep reading there is no way to delete things on BaseCamp. This is insane. Hate BaseCamp, which I'm sure many people feel the same way. Haven't been able to find anything on their support pages. I wouldn't think the one map would take up my 7GB storage on my device.
This isn't a BaseCamp issue, which I've used for many years and find it excellent. It will delete data on handhelds without any problem. On the road devices handle data differently and data can only be deleted either by using the menus on the device on via Explorer.
Your post though is confusing. You say when you plug 'it in' but which device are you referring to? How does BaseCamp show your internal storage as being close to completely full? Exactly what data is showing in BaseCamp that isn't on your device?