Hard to tell, where is the problem. Was the size exactly same as size of the file you've uploaded? If there is few bytes difference, problem may be that one of you have transfered file in text (ASCII) mode, which corrupted it. I have no other idea now.
I'm sending a client's entire QB company file to him monthly. It used to go okay via e-mail but won't any more (perhaps due to new firewall or file may just be too big for my ISP to handle) (I live in the sticks).
I've put WinSCP on my machine and had him put it on his. I was able to drag and drop the file from my Desktop to WinSCP. He was able to drag and drop it from WinSCP to *his* Desktop. Icon showed up on his Desktop and Windows Explorer showed the file in Desktop with correct date, time, and size.
However... When he tried to use QB "Restore" command to up date his QB with the new file, QB told him - repeatedly - that it could not "find that file on that drive" - pick another one.