Hello janer,
I hope these screenshots will make myself clearer..
This should be the main page you see when entering the editing page of a submission:

- Editing stage: Main page.
- editing.stage.main.page.png (15.7 KiB) Viewed 748 times
You have the option to upload a new galley file. This means you can have as many versions of the paper as you wish.
Usually used to offer readers multiple formats (PDF, HTML, Videos, whatever...)
Once you have uploaded a file, you can always go back and edit it, to make changes or replace the file.

- Editing stage: Editing a galley file.
- editing.stage.galley.png (9.91 KiB) Viewed 748 times
I don't think OJS will reset the counters if you REPLACE the file when clicking the EDIT link beside it, instead of uploading a NEW galley and removing the previous one.