why replace the file every the time to save changes such as highlighted text and comments

I am reading content in pdf file on daily basis, highlighting some key points every time for future reference but i need to replace the file with same file name to save highlighted text and comments.

But why save option prompting save as every time, what is the difference in between them? Is there any possible way or setting to save highlights and comments in the same files instead of replacing the file with same file name.