I would start with training for SA or another position whilst the player is still at 58, 78, 98%. Then during the last couple of days of the season pause the training to let him reach 59, 79, 99% and show on negotiations list. BUT as soon as he's at -9% un pause SA or other position training.
Once I had a player on SA training at 99% who without playing a match or receiving a skill point as a gift from friends still managed to reach 100%. Response from support was that even though he was training SA some percentage of his training would continue to be added to his abilities and not just towards a special ability or other position.
I'll even stop training players completely if I think there's a risk they'll reach 100% eg a 3 position player with a special ability.