Flash Tool would be software tools for building new ROM images. A new application for this is currently under development. However, to have this on the console, the original BIOS chip must be replaced with a new chip with a custom ROM. Examples of chips that work are: MX29LV320, MX29LV640. These are the ones I use, but I believe others can also be used. You have to check the datasheet.
The original PS2 ROM chip cannot be re-flashed.