Just and update, SCT managed to restore my stock file and all is working now.
Here's a summary of the process:
1. Create an account and open a ticket on - SCT's support page
https://derivepower.freshdesk.com/support/login
2. They'll ask for general vehicle info including, year, make, model, engine size, vehicle vin and ECM strategy - you get the last two by plugging in your SCT device and select vehicle info.
3. They'll do what's called an Infield Recovery by using your stock file that you would have saved beforehand. To save your stock file you need to use the SCT device updater -
https://derivesystems.helpjuice.com/sct-software/353181-device-updater - there's a button there that allows you to save the stock file. This will be in a .bef format which you should email to yourself or save in a safe place.
4. Once you send SCT your .bef file they'll send you a back a .cef file which you'll then transfer to your SCT device using the device updater software from the previous step.
5. At this stage there was a bit of back and forth because I guess the file wasn't reading properly and I was getting an error - Ref #11020
6. I was then told to plug in my SCT device into my laptop again and choose "Automatically Check for Updates".
7. From here I got a a prompt that says recovery is loading to the device which took about 5 mins to update.
8. After a bit more back and forth using "team viewer", the SCT team was able to load the stock file back on my new LiveWire TS device. From there I was able to flash the stock file back on my vehicle.
Thanks SCT support team!