I agree with leaving the dished stones as they are.
However ,to flatten a stone, you use a dressing/flattening stone. In Japanese it is called an arato...litterally "Rough Stone". You can buy modern dressing stones from Woodcraft and other woodworking suppliers. It is a coarse grit ( usually 100 or less) synthetic stone with grooves to make it cut faster.
http://www.woodcraft.com/Catalog/ProductPage.aspx?prodid=17629
Work the stone to be flattened on it until flat. Carefully clean the dressed stone to remove any coarse grit that may get on it.
A 100 grit diamond stone will work to dress a finer stone,too, but you have to watch for diamond crystals getting embedded in the finer stone.
To recondition oil stones, you first have to remove the metal, dirt,and gunk out that has dried in the stone pores. A good scrubbing with a bristle brush and brake cleaner or paint thinner will do a lot. Most of the time this is all that needs to be done. After the cleaning, dry the stone for a day or two, and then soak in light oil to re-fill the pores with oil.
On severely caked and age dried stones ( I have seen them that look like they were packed in Cosmoline), after cleaning with solvents, the stones can be simmered for an hour in a solution of dish soap and water. After this, scrub them well by hand with dish soap and water. Rinse well and wipe dry. Bake in a 250 degree oven for two hours. Turn the oven off and let the stones cool in the oven overnight. Re-oil and they should be good as new.
Stacy