What protocol are you using?
step by step description of the event
a. connected to remote client using winSCP version 4.2.7 (build 758)
b. waited some several minutes.
c. Internet connection when down (disconnected) (i was not aware of the Internet disconnecting)
d. attempted to copy a text.php file of about 50K from the remote directory to a local directory already containing the file.
e. copy process started
f. the local copy of the file was overwritten to a size of 0K (zero-bytes).
g. winSCP prompted me that connection to the remote directory was lost
h. the file in the local directory disappeared (deleted).