Assuming you're just playing it in the background of something else you're doing or putting the theme to your own visuals, it should most likely count as transformative under Fair Use regardless of who owns the copyright to the song. The current copyright holder to Thomas the Tank Engine and his theme is
Hit Entertainment, owned by Mattel.
You can appeal copyright claims on your videos in your video manager, after which the copyright holder has 30 days to retract its claim or deny your appeal. Should your appeal be denied and you still believe that the claimant doesn't own the copyright they're claiming from your video, you can file a
counter-notification with Youtube. Even if you're still using copyrighted work, you should be able to file a counter-notification for false claims if the claimant isn't the real copyright holder.
