I think there may be some overthinking going on here. I suspect MG's right that this is just a basic check of slips. My cursory reading leads me to think you're OK with what you've done -- you claimed tuition 'to the extent' it was not reimbursed. You claimed the 50% that was not reimbursed. That's my reading and what I would go with. If, technically, that was incorrect and CRA pushed the matter, I would just include the 50% reimbursed in income (doesn't matter that it wasn't on the T4, you can add if as other employ income) and then claim 100%. I doubt it comes to that.
Just submit the slip and note that you've reduced the claim by 50% as you were reimbursed that amount.