dc333 wrote:

Even though "Delete Files" is unchecked, the synchronization checklist will flag a file for deletion on the local side because it does not exist on the remote side. I am trying to set local as the target.

But they are not checked. As documented:
https://winscp.net/eng/docs/ui_synchronize_checklist#selecting_actions

In addition, the "Use same options next time" checkbox doesn't save the Target Directory option, it simply reverts back to remote the next time I open the synchronize window.

Yes, the checkbox saves the options only, not the directories.
If you want always to synchronize the same directories, you can create a desktop shortcut or script for that.
https://winscp.net/eng/docs/commandline#operations

Using the latest version (5.19.6) in Commander Mode in Windows 10.

Even though "Delete Files" is unchecked, the synchronization checklist will flag a file for deletion on the local side because it does not exist on the remote side. I am trying to set local as the target.

In addition, the "Use same options next time" checkbox doesn't save the Target Directory option, it simply reverts back to remote the next time I open the synchronize window.

I just started using this program yesterday so I may be missing something.