When a project retires, and a users' CPID changed, the connection with the retired project account will be lost, and the credits will not be included in the combined account.
I think there are ways to prevent this, but it will be difficult. It may be possible to match a CPID from the XML file (of a living project) against the existing CPID in the stats DB. If they differ, update the 'old' CPID in all retired projects. While this is doable, it may put too much strain on the server (you must have read about the struggles I have to keep up with the growing userbase).
Another option is using an AMS (
link). Once a project is included in the AMS-account, the AMS user could update a retired project him/her self when the CPID changes. But this will only work if the AMS works together with BOINCstats

(some people will know why that smiley is here).
BUT: with the way CPID's are handled now (oldest CPID always wins instead of highest CPID) this shouldn't be a problem at all. Once established, the CPID will remain the same forever. A new project could have a different CPID, but will line up with the older one. The catch: you need to use a v5 client or higher.
Please do not PM, IM or email me for support (they will go unread/ignored). Use the forum for support.