Okay, let's say you have a local folder named folderA and a remote folder named folderA... Local folderA contains 3 sub-folders: folder1 folder2 folder3 Remote folderA contains 5 sub-folders: folder1 folder2 folder3 folder4 folder5 When I upload local folderA to the server, and select "replace" (with "apply to all") checked, will it delete folder4 and folder5 on the server because they aren't on the local machine? I recently upgraded a (simple machines) forum, and a lot of deep sub-folders and files came up missing. Things like uploaded user Avatars, and a custom theme I had created. The files were on the server right before the upgrade, and missing after it. I'm trying to decide if I should blame Transmit or the forum upgrade package.