You have to guard against conflating issues. The key to unravelling seeming complicated matters is separating the issues as much as possible.
Why are you holding an appeal hearing that requires the attendance of the appellant? The basis for the appeal should be set out in the appeal and adjudicated on its merits.
I suggest deal with this separately under normal attendance rule procedures first. This will help inform any potential consequences i.r.o. attending the hearing.
The employee is entitled to take up the matter through the CCMA. Invoking one's right to take a dispute to the CCMA seems premature as there is still the outcome of the appeal to be given, but if you are not going to amend the finding, there seems little sense in delaying the inevitable by pointing this out at this stage.
The onus is going to rest on the employee to prove that allegation as true on balance of probabilities. That should be a lot easier said than done, particularly if it is untrue.
Do you have a policy in place that deals with this?
I think Sakkie covered the problem here already - it helps add credence to an allegation of victimisation. I suggest you should only use this point as a counter-argument in the event that the employee introduces your knowledge of the emails as part of their evidence.
The good news is that there is no dismissal at this point, so when it comes to awards (if it comes to that), the worst bullet you need to avoid stepping in front of right now is an adverse award on costs.
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