As long as the report is the same name and it is being published to the same workspace it will overwrite. This maintains the report's GUID (internal identifier) which is also used in the hyperlink to the report, so is handy to keep constant.
You can test this by publishing a report and opening it once published. Check this link and the report content. Change the report and publish again - it will ask you to overwrite. Once re-published, you can refresh and see the report link stays constant but the report is updated.
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…