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have something similar with cloudrun for some setups. (not all some though).
i was able to work around it with appending `--refresh`  . `pulumi up --refresh`  not sure if it helps in your case ?

I experienced exactly the same issue you're describing, made a protoype in one big file, extracted to components and when now trying to create a stack from scratch using the refactored code, I get the 409 error. Tried also going back to the old code and now it's not working