Potential source of the problem and solution
As a developer I asked pointed out, the problem could be that I upgraded drupal core but in my installed version my initial profile "atlas" was still marked as active. He recommended
a) to set in the system table status=1 for the "standard" install profile
b) in the variable table change the install_profile to "standard".
This is also described here: http://flipbit.ca/2012/05/drupal7-fix-install-profile-name/#20120518solution
I tested this and it worked. An upgrade after changing these two parameters did not disable the theme.
So, this worked for me. I am not programmer and can therefore not judge whether this is the final bug fix or only a fix by coincidence. Reading the many discussions about installation profiles and how they are designed in drupal leaves some open questions....
One user also asked whether I replaced the profile-directory during the udpate. I did this. I tested it without replacing, but the problem remained.
Unfortunately I could also nowhere find clear information about how to disable a profile. In my case I used the profile only for the first installation but will not use it in the future anymore.