I had SFTP evrsion 4.16 and I was using scripting to transfer file toward a unix system.
The script says so :
option batch on
option confirm off
option transfer binary
Log file shows a binary transfer too.
Since it is a binary transfer I would expect that WINSCP would not try to do anything with the CR and / or LF.
But indeed every 0x10000 or so, a CR was added to the file I transferred. Since I suspected first the remote server I locally installed a SSH server for windows. And i got the same behavior with a binary transfer to 127.0.0.1.
Switching to version 4.21 beta stopped the behavior, but it might be worth having a look what provoked this.