Hi there!
The issue sounds like a transmission error. Do you know if the files were transmitted via text-mode or binary-mode? You can check for a transmission error by comparing the exact size (in bytes) of the savefolder between the server and your pc.
In the case of a transmission error you can try the following:
be sure to use binary mode transfer
transmit the savefolder as zip or tar.gz and unzip it on the server