It's positive that you are already going through mediation. It's an important step to trying to find a resolution.
Unfortunately, a mediation agreement is not legally binding, and there is not yet a court order in place.
So technically you both have equal rights at this point, and no-one can stop you from collecting him if this is what you wish to do.
The issue that you may find is that if there is a confrontation at the nursery, it will be you that comes off worse. Nursery staff may side with your ex if they are more familiar with her, she may also play the victim card. She may be trying to goad you into a confrontation to use this against you in court.
My advice in these situations is always to err on the side of caution - she does not have the right legally to dictate when you can and can't have your son, or change agreements last minute, but unless there is a court order in place it's simply a case of your wishes against hers. Dads nearly always come off worse in confrontations and public arguments. It can also be upsetting for the child to see their parents rowing in public.
If it's usually your day and the nursery knows this - you could consider turning up early (having telephoned) to collect him in advance. That avoids a confrontation. But be aware it could provoke a reaction and she might stop all contact - which you cannot do anything about until you are in court. It's not fair, but I'm afraid this is the reality that many face in your situation.
Until you have a court order, there's no way to enforce your contact or punish your ex for changing the plans without your agreement.
Ultimately this is your call whether you go to collect him, but I have set things out for you so you can make an informed choice.
Hopefully, I have answered your query in a way that is simple and easy to understand. If you have specific questions arising from my response, let me know and I’ll happily clarify for you.
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