Syncing prototype in Sharepoint, overwriting, updating new pages

I am working with a client that has been using Axure for a while and has a great deal of work already done in their prototype, Apparently, the current prototype sits in Sharepoint. This version of Sharepoint doesn’t allow mass updating of a nested folders. I can’t just drag over a folder of an entire HTML Axure-created prototype because I’d have to manually recreate the folder structure and move files individually. The firm is working to get Office365 rolled out where OneDrive does all the sync-ing automatically and, at minimum, I can drag multiple folders over.

The company has strict IT policy that won’t allow Axure-hosted prototypes or anything of the sort. I was told if I change one page in a prototype and none of the links change, just the layout on the page, that to drag just the updated file and overwriting it will not work. It will break the original prototype.

Does anyone have any familiarity with this scenario? Is there no other way to go about this than manually dragging over specific files? Even If I do the update-only-new-files method, there’s a lot of room for error. And it all rides on the assumption that the new page is only a change in the body container with no new links or changes to header and footer.

Thanks in advance if anyone can help!