Let us start understanding what happens when you press on the deploy button:
When you click deploy Cloud9 will run aws cloudformation package and also aws cloudformation deploy on your template.yaml file in the background.
Now all your files will be bundled into one serverless application and there is only one CloudFormation stack they can only be all deployed at once with CloudFormation.
If you're only make a code change for one function and are not modifying any configuration settings then, you could update that one function from the command line with the command shown below
zip -r - . | aws lambda update-function-code --function-name <function-name>`
Note: Run this in the same folder as your template.yaml file, and replace <function-name> with its full generated name say cloud9-myapp-myfunction-ABCD1234