Running the Toolkit will change the vendor on the PO as well. You really need to talk to your Adagio Dealer because this sounds like the configuration needs to be corrected as well as the data.
Steve's suggestions are correct to deal with manually outside of POA, except you cannot have a sundry vendor with the same code as AP vendors. By design, this was disallowed so that there would be no confusion over haveing the same vendor in sundry vendors or Payables Vendors.
I suppose you could leave and hope that eventually the problem will go away, if you like to keep data integrity issues in your data. It wouldn't be our first choice.
I might also suggest that if you (or your staff) see errors appearing on the entry screen(s), you might deal with them at the time and call for support instead of forcing them through. Hoping that the error will safely land is not normally the best practice, and will cost you more in the long run to correct.
Brian