As far as I can tell (I couldn't really find any documentation describing, or even admitting the existance of it) SFTP resume assumes the part of the target file that already exists is identical to the first part of the source file, up to the size of the remote file. Then it appends the rest of the source file behind the existing target file, and assumes that the two files are now identical.
This fails if the part that was first transferred changes in either file before the transfer is resumed. I guess your
.mov file has some kind of header in the very beginning of the file that is necessary to play it, and this is not written to the file until the encoding is finished. Then the remote file you have copied will miss this header, as it was not written yet when it was transferred.
Other tools like
rsync have the capability to detect these things, and in some cases avoid retransferring the whole file, at least if the late change is merely overwriting and not insertion.