Neil Gaiman, comics luminary and occasional Doctor Who writer, has provided something of an answer for one of those questions that casual Doctor Who fans and those of us on the outside looking in have been asking themselves since it was recently revealed that there was somewhat more to the history of The Doctor than was previously known: Does John Hurt's War Doctor "count" in the numbering of The Doctors? Should we begin referring to Matt Smith's Doctor, for instance, as the Twelfth Doctor rather than the Eleventh?
Gaiman, fairly emphatically, answers those questions as yes, and no. You can read his answer on his Tumblr, or embedded below, written in response to the question "Is the War Doctor now considered as the canonical Ninth Doctor?"
I don’t really understand the question. I’m tempted to say something like, “No, the John Hurt War Doctor is just something that happened in THE NAME OF THE DOCTOR, THE NIGHT OF THE DOCTOR and THE DAY OF THE DOCTOR on television.”
If it happens on the TV, it’s canonical, unless it isn’t. (For example, no-one seems entirely sure whether we get to see pre-Hartnell regenerations during the mindbending battles of Brain of Morbius.)
We now know there was a regeneration between the Paul McGann Eighth Doctor and the Chris Eccleston Ninth Doctor, one whom The Doctor himself has only just begun to regard as being The Doctor (as opposed to being something else).
If you mean, “Do we now all have to agree to renumber all the Doctors?”, I think the main purpose of numbering things is to communicate, and we all know who we mean when we say Doctors Nine, Ten or Eleven. If anyone corrects you and says “You mean TWELFTH!” when you say “Matt Smith was the Eleventh Doctor” then that person is being irritatingly pedantic and should be pitied, in a nice way and with a gentle friendly, not-patronising sort of love, because they will have long hard lives ahead of them.