I've not used the 6pin header before, but can I use that to load a Leanardo USB bootloader? (if that's the right terminology).
Yes, you can, and yes that's the correct terminology. However, I don't think it will be necessary to do that. Try this:
Press and release the reset button on the LilyPad USB.
Select the port of the LilyPad USB from the Arduino IDE's Tools > Port menu. You need to wait a second or two for the port to be enumerated, but you also need to do this before the bootloader times out, so the timing is a little tricky. Note that the Tools > Port menu only updates after you close the Tools menu, so you can't just leave the Tools > Port menu open and wait for the port to appear.
Select the correct board from the Arduino IDE's Tools > Board menu.
Sketch > Upload
Watch the black console window at the bottom of the Arduino IDE window. When you see something like this:
Sketch uses 444 bytes (1%) of program storage space. Maximum is 32256 bytes.
Global variables use 9 bytes (0%) of dynamic memory, leaving 2039 bytes for local variables. Maximum is 2048 bytes.
press and release the reset button on the LilyPad USB. The upload should now finish successfully. After that, the board should be fixed.
You will probably not be able to use the Arduino Web Editor for this, because it won't allow you to start an upload with no port selected. So use the regular Arduino IDE.