I think that's what would happen. Everything for the ninth and tenth Doctors happened to the Doctor, but like the Year that Never Was, no one remembers it other than the people at the heart of the vortex.I'd be ok with a reset button à la 'Last of the Timelords' - it didn't happen, but for the people we cared about, it did.
Does that include people like Sarah Jane and Jack Harkness? As I suggested earlier, if everything the Ninth and Tenth Doctors did no longer applies, then Nine and Rose could never have met Jack; Ten could never have met Sarah Jane. There are all these problems.