Hi
Basically you will need to rename the file on BIM 360 and then you can either move to an archive folder or leave where it is, this will ensure you have the history and it's retained.
If you copy it to another folder you'll delete the history.
If you move it to another folder the history is retained.
Once renamed you can then upload the new file with the old file name.
If you don't need the history then you can delete the file.
You Cannot overwrite the file as you would lose the history the same as you would if you did this on you local server, if you 'saveas' central on your local server you'll delete the backups and history.
When we need to preserve the history and issues and markups we rename the file, then we upload a the new file with the old file name.