Proteus/Ares - how to scrap old layout but keep Isis schematic
I assume you refer to version 8 where the schematic file (.dsn) and board file (.lyt) are stored in a single project file (.pdsprj).
The simplest way I can think of is to create a copy of the project (as a backup), and then in ARES use the selection mode (arrow icon in the top of the left side menu) to select the entire board and click delete. Then you can start the board from scratch.
You can also delete selectively only the tracks (keeping the component placement) using the track mode.