the Doctor wasn't "wiped from history". He was excluded from the restored universe -- until Amy remembered him (in "The Big Bang"). What had happened had still happened, even though some of those involved had forgotten about it.
To add an example to this, it works the same as it worked when Rory was excluded due to going through the crack. In general he was forgotten, but pieces (such as the ring) were left behind.
Another example is Amy herself, who continued to exist despite her parents having been erased by a crack.