Unfortunately no, this is not possible and it's not how Import is mean to be used. Import is only for initial import.
The issue with repetitive import is that there is no way how to correctly keep all things in sync.
One example is what you already figured out. When importing deleted entity, there is no easy way how to decide if this entity was added to Skipper or removed from the code.
The event worst thing is all arrays/lists/sets ORM variables where is very difficult to correctly merge such values.
The issue is that there are so many items which don't have unique identifiers and because of that it's difficult to merge/re-import it.
We already tried to implement this feature some time ago but we decided to reject it because of these reasons.
It's much better to improve editing in Skipper than implement re-import feature. We already implemented lot of copy&pastes of all entities, standalone fields between entities, etc.
In case you miss anything, feel free to write your use case and we can try to improve editing in Skipper.