My Citicard Mastercard recently sent me a new card, even though the one I had did not expire until 2016. The new card had a chip with electrical contacts (no RF), and it had a new account number. It had the same 2016 expiration. Upon "activation", the old card got deactivated. This card swap was due to identified risks-- probably the stories about Target, Home Depot, and many more having their card info hacked. I was glad they took this proactive step. It did make some work for me.
I download that account into Microsoft Money using PocketSense. I had notice some strange "transfer" credit transactions during downloads for a couple weeks, but did not pay attention other than checking the Citicard web site to make sure that these were not somebody pulling money. Since they were credits and not charges, I did not worry further at that point.
Citicard had created an account also accessible under the same Citicard login. The transfers were transferring what I owe from the old number to the new number. Makes sense now. The old account shows a zero balance. I did not create a new account in Money; I just changed the account number and continued in the same Money account.
In Pocketsense I wanted to start downloading from the new account rather than the old. I could have used setup to delete the old account and add the new one. Instead I edited ofx_config.cfg with a text editor (not a word processor) and changed the old account number to the new account number. Then my next getdata got transactions from the new account. There were some duplicate transactions. I would have avoided the duplicates by switching the download sooner. But I just voided one of each pair. When done, my Money balance matched their balance, so I marked the transactions as reconciled. I voided all of the card-to-card transfers. Had I left them un-voided, I am confident they would have canceled out.
This is just a general description. If anybody want something more specific posted, let me know. I would expect that other US credit card companies will be doing something similar.