At this moment it is possible to delete a script from a managed solution (via make.powerapps.com). It creates an unmanaged layer, but after removing the unmanaged layer, the script becomes 'visible' again in the managed solution, but without code (this was empty).

It shouldn't be possible to delete a script from a managed solution or otherwise, removing the unmanaged layer should result in a situation where the script is available again with the original code.

Now the only solution is re-importing the managed solution.