No it is not, it is only mentioned once (48.24) , as the "Valley of Mecca". 
You're right; it's only mentioned once. But it's not the "valley" of Mecca. The phrase is "fi batni Mecca", which literally means "in the middle of Mecca". Many translations support this. Eg:
"And He it is Who has withheld their hands from you and your hands from them in the midst of Makkah, after He had made you victors over them. And Allah is Ever the All-Seer of what you do."Dar-us-salam.comI really have no idea how 'batni' can mean 'valley'. 'Valley' in Arabic is wadi', which is mentioned several times in the Quran, eg. 8:42, 14:37.
I am pretty sure he is talking about Mosques in the conquered territories, places like Mesopotamia and Iraq, which were only conquered after Muhammad had already died. So based on the traditional chronology it could not be mosques that were built before Muhmmad supposedly changed the direction of prayer.
He didn't mention any dates, nor did he even provide a location of the mosques with the different qiblah he was talking about. The only piece of evidence he provided was the ruins of a mosque in the middle of the desert.
Well if that were true then that would be fascinating new information to me. There are not "many accounts" of a city called "Macoraba", I have heard that name somewhere before and a tenuous connection of Macoraba to Mecca, but nothing conclusive. Over here I have provided tonnes of Classical descriptions of the Hejaz region, none of them mention Mecca or Macoraba. Anyway if you could provide a source for this "Macoraba" that would be really appreciated.
You can find plenty by just googling something like "Mecca Roman Bezantine" or "Macoraba Roman Bezantine". 
Here's one.Perhaps. But surely oral accounts transmitted over a period of 200 years (quite a few generations in those days) are particularly amenable to modification? I could understand why a historian would not want to build a picture of history based on them.
Of course they are amendable to modification. That doesn't mean a historian should dismiss them all. A thorough study of the evidence should include the examination of the origins of each source, both written and oral.