Hi Mark Poole (7805)
I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Issue:
Effect of editing custom Azure Policy definition on existing assignments?
Solution:
The only way I managed to get this resolved was to remove the AMA client from the machines and create a new remediation task. The client was then redeployed with the correct settings.
If you have any other questions or are still running into more issues, please let me know. Thank you again for your time and patience throughout this issue.
Please remember to "Accept Answer" if any answer/reply helped, so that others in the community facing similar issues can easily find the solution.