ayachan - to keep the same ID, go to Admin Home > File Galleries and check Keep fileId for archives.
The Action icon popup for files in file galleries has a "Replace" action. I didn't test this, but suppose that it allows replacing the file and keeping the same ID.
In my version (6.3) I don't have a "Replace" but an "Upload New Version" that I expected to do what you say, but not. Actually creates a new id at the same place (links in pages maintain the original - bad - id). I do not know which is the expected (designed, I mean) behavior but it could be a bug.
If it's necessary to maintain the original file for restore purposes, maybe the original file could be indexed with the new id and use the old for the new file.