I ensured the directories were correct, and that 'delete files' was not checked (to be safe), all other options were set to default.
I hit synchronise, was presented with a window with checkboxes next to the three directories in the remote location. (local location was empty). I went ahead and a_ssumed these were the 'changes' to be reflected and clicked the checkboxes and hit Okay.
.. And then all my remote files were deleted.
This program isn't very intuitive, is it?
PS: "A s s u m e d" is filtered by the forum's language filter?.. o_o