I will note that I am able to confirm that if i manually upload the file into azure and it has the correct path as the name, it works (if i upload the file 07251437-f314-4adf-b4ef-09a91bc4155e.txt that is in the blanksite/files/07 folder, and name it "blanksite/files/07/07251437-f314-4adf-b4ef-09a91bc4155e.txt" in azure, i can delete it from local and the permalink will find the file on azure).
It's a work around but hopefully someone knows an easier way, otherwise i'll have to create a migration script (which won't be too terrible, just scanning files of the site folder / media folder and uploading to azure)