I have set the filter to be "IsMaster=True" but i get no objects shown
Please describe the issue more clearly, e.g. what exactly steps you are performing, what exactly objects do you mean, send us screenshot which demonstrates this issue.
If restoring to a different connection is only valid of "Insert Records" do I need to clear out all existing records first? How do I do that?
You can use Query Tool for this. Open Query Tool, select New SQL and then select the necessary Dynamics CRM connection and perform delete query for the necessary object, for example:
DELETE FROM your_table