Like the title says, after Clear Cache my uploaded images (/mytheme/assets) get deleted. The path to the file is still there, but the file itself is deleted from the server.
The asset folder from grav is not intended for uploading your own images: https://learn.getgrav.org/basics/folder-structure#assets
I did that for a full day until I figured out the bigger picture 
@chris_jung, 
I thought this just applies to the root’s assets folder… Thank you for the hint!
There is a setting in system.yaml:
cache:
...
clear_images_by_default: true # By default grav will include processed images in cache clear, this can be disabled
Set this to false, and your images won’t be deleted with regular cache clears.
My fault I misread that /mytheme/ - Thing.