How has any one enrolled vendors in commercial card payment program?

We are soliciting vendors to participate in commercial card payment programs. One of the items that came up was handling 1099 reporting.  Since a vendor could enroll in this program any time of the year, once that happens what setup needs to be done for 1099 process to not include payments made through this program?

Creating a brand new vendor setup on enrollment was an option but that would mean losing history.

Any insights?