I was using the code pipeline and github webhook to deploy code change for a while and this issue never come out until these few days.
And I also download and verified the code conent is also sync with the github repository.
But when I login through ssh and check my root directory it still the latest version as I pushed few days ago.
The Event logs show everything is successfully deployed
I also did download the zip file and try the manual "Upload and deploy" on the environment but it also the same.
And I also follow the thread to check on the termination protection and it's not enabled in the instance.
End up I can only through the ssh to update the file directly.