Getting an error that a flow "was" activate and cannot be overwritten

Once activated, a flow version can never be modified. In fact, about the only reasonable approach is to delete all paused interviews, deactivate the current flow version, delete all references to the flow, delete the flow entirely, then deploy the flow and all its references back in place.

This restriction exists because if a flow was active, it could have paused interviews or interviews already in progress, and so changing the flow's properties could invalidate those interviews. This is obviously an undesirable state since users would lose data, but it'd be a lot handier if Salesforce would simply check to see if there were any paused or active interviews and allow deletion or modification of a version if it's reasonably safe to do so.