WARNING: Do not use the synchronize function, ever. It will DELETE your files even if you don’t want

The synchronize function is broken.
Cleverly hidden somewhere in the settings is a “delete” option. It’s a good idea to hide it, because if you disable it, it will merrily delete your files.
The synchronize preview is ambiguous, too.

Can you provide us with step-by-step instructions to reproducing the problem?

What hidden "delete" option are you referring to?
There's only Delete option clearly visible on the Synchronize dialog:
https://winscp.net/eng/docs/ui_synchronize
And it's unselected by default.