Hi Nikki,
After spending a bit more time with the team, two possible workaround were proposed. I have not been able to verify these myself, so sharing in case either is an option for you.
Rather than exporting an Animation Sequence, try exporting a Level Sequence from the MetaHuman Performance asset. This applies the animation directly to the Identity Rig, which should avoid having to bake back to Control Rig.
Or, leave the Animation Sequence in Sequencer, but mute the track. This would then show the timecode as you polish using the Control Rig.
Appreciate neither is ideal, but perhaps they help as a workaround.
Mark.