Re: Need to adjust existing relationship in canned app - is this safe to do?

If you have existing data that is utilizing the current set up..
I'd leave the existing relationship, and create a new one to the opportunity.

Then you can easily and appropriately connect the opps to the lead source.

However, if this is a brand new app, and you are starting fresh, then you shouldn't have any issues by deleting the old relationship and building a new one.