I love this plugin and just recently ran into my first issue, basically I’d need to reset the plugins posts, in order to switch he main blogs.
Just as info and “cheesy workaround” I’ll post how I solved the issue.
I simply set the max number of posts to  and created a “test” post. By reaching the new limit of “1” post all older “Sitewide Tags” posts were deleted. Now I deleted the test post again and it was as if the plugin had never existed.
However I think it would be a nice upgrade to be able to “reset” the plugin posts via the interface.