Unfortunately you are stuck here, I am afraid. The rules (IRPA states it as law) state he must identify any children of his, accompanying or not. This also means they must examine those children for admissibility while processing his application. This includes a medical and could include an interview as well.
Failure to disclose would be misrepresentation. Failure to submit to examination would result in longer processing times. If his ex fails to submit his daughter to examination, then she will be forever excluded from family class sponsorship in the future.
The logic is: if there is a material change in circumstance, and she may require to depend on her father or seek entry, that she has been examined. They don't want to process the same people over and over. That would be a waste of resources.
In this case, they know she isn't coming. But she still needs to be examined. So he should try to explain this to his ex. It's a formality and means little to their daughters' situation for now.
Sorry for the bad news. I hope it helps. Best of luck!