Comments and Highlights are retained in the document if the file is replaced. Just remember to use the Replace file function instead of Delete.
How comments and highlights remain after replacing a file
When you add comments and highlights in a document, they will be kept in an invisible layer upon the document. This means if you make highlights on page 3 then the highlights will remain in the layer upon page 3 and are not fixed to the document.
If you, for example, change the text or remove some of the text on page 3 and replace the file with a new version, the existing highlight will remain exactly where you placed it in the layer - even though the text you highlighted has changed.
Is it possible to lose my highlights and comments when replacing a file?
The short answer is Yes.
Here is a scenario to explain:
Let's say that someone has uploaded a file of 4 pages in FirstAgenda. In FirstAgenda you create highlights on page 4 (which are actually placed upon the layer of page 4). Then your colleague replaces the file with a new version where page number 4 is deleted. All highlights and comments in the layer of page 4 will no longer be visible because page 4 doesn't exist anymore.
Furthermore, if a third version of the file is reuploaded and again consist of 4 pages (a new page 4), then your highlights in layer 4 will reoccur on the new page 4.