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Reset device list
For anyone that has this question in future.
As it seems there is an issue on Apple's end since paid accounts can have up to 100 devices and free accounts can have "much less". When going from having a paid developer account to a free account all devices attached to your developer account remain unless you remove them before you membership expires (I assume so you don't need to re add them when you re-subscribe).
The only way to resolve it is to get Apples Technical Support to remove the devices that were assigned to your paid account (Since free accounts cannot access the add/remove device section the website) or again sign up to the paid developer program.