OK, you are correct, but this is only due to the phrasing of my last comment and not because of the quality of iCloud syncing. MobileMe was MUCH better in this respect! It DID offer the option to overwrite the data WITHOUT the need to manually delete before.
In addition, this was not the core point.
The main point is that iCloud for (at least to me) unknown reasons did stop performing its job for the bookmarks that were synced before.
I would like to know if there is an option to trigger syncing, without the need to delete manually, and then switch of and on again.
Again, the question is:
What can one do to force syncing in a way that avoids the merge?
I have found another way of doing this using Xmarks
* On iOS device - turn off icloud syncing for Safari - and delete from device
* On Mac - turn off iCloud syncing in settings
* On Mac - turn back on iCloud syncing and select Merge
* On Mac - re-download backup from Xmarks by doing sync download from Xmarks
Hey presto, you have correct synced copy back in the cloud.