Files deleted or modified between git revisions are automatically getting deleted from instances

CodeDeploy is designed to deploy applications, not simply copy a specific and constantly different set of files.

As such, before deploying each 'revision', CodeDeploy will first cleanup any files deployed by the previous revision. Let me explain.

So, let's say the previous app deployment uploaded three files:

File AFile BFile C

And then the next deployment only included these files:

File AFile C

Code Deploy will first cleanup the 3 files it deployed on the first revision (A, B and C), and then deploy your new revision... It never simply uploads the files intended, it always cleans up the old files first (determined by looking at the previous 'revision'). This is important because it sheds some light on what seems like mysterious behavior in your case. The result, after deployment is, of course:

File AFile C

Now, it gets interesting if you've manually added files into the mix outside of CodeDeploy. It will only clean things it knows about, and it also won't overwrite files in the current revision if this cleanup phase doesn't remove them. This is often seen when people have manually installed an application, and then tried to do a CodeDeploy to the same folder... there's no previous revision, so nothing to clean up, and then it tries to copy on top of the existing files and will error out. You typically want your target folder to be 'naked' so you can start the revision history properly.

For example, in that previous scenario, if you had previously uploaded the Files A, B and C manually, then the deployment of Files A & B would have failed because it wouldn't know to clean up A, B and C first, and it would then give you an error trying to overwrite the files A and B.

A file (or folder) completely outside the deployment... i.e. not part of either revision, say File D... would be untouched and remain happily there both before and after the deployment without complaint. This is useful for placing data files and such things that may be specific to the deployment but aren't necessarily part of the code base that you don't want to constantly redeploy.

Now, you can do lots of interesting things using the hooks, of course, but it feels like the wrong tool for the job at hand. The hooks are intended for doing things like stop/start services, etc. not to manage the file copy management that is at the heart of what CodeDeploy should be doing for you.

Excluding all files from the app spec (i.e. no files specified) and simply using BeforeInstall and/or AfterInstall steps to perform the copy logic is an approach that may work for some scenarios.

In any case, maybe this better understanding of how CodeDeploy operates might help you craft a solution. I don't think its particularly well documented. My understanding comes from observing and struggling with it myself.