I did a factory reset to it which for some unknown reason erased the 2 firmware updates I had done since purchasing the unit a couple years ago. - Is this normal?
Yes. On a Lacie a factory reset actually restores the box to the state it had when it left the factory.
About your problem, you can try to delete the folders via ftp. Another option is to rename them, if you have the right. When you rename them to a name starting with a dot, it is possible that you won't see them anymore. (A file starting with a dot is 'hidden' on Linux boxes).
And else, yes then you need ssh, I'm afraid.