Ok, ive been playing around whilst writing this and made a discovery.
If i use the Camera Stand Visibility toggle to hide everything except the mouth layer, then clear the cache, close Opentoonz, reopen, redo the lipsync. Then it worked. At least that time that i just tried it. Not the most elegant solution by any means, but its a solution for anyone else who might have a similar issue.
P.s - DarrentT, Great Youtube tutorials by the way, they have helped me a ton!