The use case is as follows.
Teams build reports and then publish then for their user community to use them. That user community add a lot of bookmarks. Teams build new versions of reports and need to replace the existing reports (to preserve the URLs). Report uses want their bookmarks preserved. It's currently only possible to do that using the Analyst Client and using the "Save As" option, and choosing the option to preserve bookmarks. It should be possible to do something similar in Library Administrator.
When using the Copy function in Library Administrator, you get presented with the dialog allowing you to replace existing reports, but you don't get the preserve bookmarks dialog\option. So for teams wanting to deploy new versions of reports - many teams will deploy\publish new versions of multiple reports at the same time - we simply need to provide more\better options around preserving existing bookmarks.
Using a Preference to control Copy behaviour may be an option to avoid another dialog
The SOAP API should be enhanced at the same time to support any new functionality so that we have programmatic options.