Thanks Russell.
However this is all hosted on AGOL.
I did however just figure it out. This process I imagine is similar to the one you describe but just accessed through the website. So for future reference:
Go to the feature service you are trying to update within AGOL layers tab.
Click on source 'feature service' which is part of the name header above the social media links.
Click on the 'replicas' link. This will only exist if there are replicas existing.
This will show you the replica ID codes. You can click on them individually to see information on them such as the username associated with it and the date it was created.
Copy one of the codes (they need to be done individually) and go back a screen and click on the 'unregister replica' link.
Paste the code into the box and click 'unregister replica'
After doing this I could update the feature services again.
However the interesting thing is in this case that the two replicas blocking the update were registered to myself and another guy. I had checked both those iPads and neither had a synced version of that map on it. So I don't know why this happened.