Git doesn't push files, Git pushes commits. (Commits contain files: each commit has a full snapshot of all the files.) The server that gets new commits then has to decide how it wants to deploy these new commits. That part is up to the server, not up to you doing the git push
.
... And then directly on the server I just created images
directory ...
If—if—the server deploys a new commit by completely removing the previous deployment and then completely installing the new commit, then your images
directory gets completely removed, and replaced with nothing.
If the server deploys a new commit in some other manner, something else happens to the images
directory you created directly on the server.
This is not a function of Git, which is not a deployment system. This is a function of whatever someone controlling the receiving Git on the server, programmed the server to do upon receiving new commits. Find out who that "someone" is; find out what they did; find out what you should to do update it to behave whichever way you want it to.