Hi Dan,
Duplicates IDs are not a good thing and will cause all sorts of grief so if you're getting them, we'd like to understand the issue better so we can find out what's causing it and get it fixed in short order. Would you be willing to zip up your project folder and send it to support@serlio.com so we can diagnose the data and see if we can determine if there's bug in CaseComplete causing this? Also, let us know any additional details on how to reproduce the issue.
Answers to your questions:
A) CaseComplete should be preventing you from creating elements with duplicate IDs. When creating a new UC, it should default the ID to something that's not in use.
B) Currently, there is no way to manually change individual IDs. Using Renumber IDs is the only way to do that.
If you do send your project files to support@serlio.com, it will open up a private support ticket that only our support team and you will have access to.
Jeff