Custom Macro causes ApiGateway HTTP to partially deploy OpenAPI spec definition

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I am busy developing a CloudFormation Macro that can create resources for observability. On testing, I've found that the Macro was somehow causing the OpenAPI spec that we are defining as a Fn::Include to somehow not have all the defined routes.

After some troubleshooting, I've set up the Custom Macro Lambda to just pass the CloudFormation template back with no changes but the issue with the OpenAPI spec persists. As a basis of comparison, I've tried one of AWS CloudFormation's built-in Macros AWS::Serverless-2016-10-31 (since I am not using any Serverless resource definitions it should have no effect and also just pass the template back unchanged), and this doesn't cause the issue.

When comparing the output from when using Custom Macro and the AWS Serverless they are the same (I did this by comparing the JSON Template from the CloudFormation console with View processed template turned on). The templates for these are the same except for Lambda Code S3Keys, which makes sense since they are from separate deployments.

Has anyone experienced this and know how to fix this or does anyone have any ideas on how to troubleshoot this issue further?

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