How to clean a whetstone?
If this is an oilstone (which is considered old fashioned exactly because of these issues), an oft-mentioned ultima ratio remedy is boiling it in soapy water. YMMV, this could destroy the stone. If you know what exact type (eg arkansas) your oilstone is, research instructions specific to that stone type.

If it is a waterstone, abrading the stone - with a flattening plate, diamond stone, another waterstone until unaffected material is brought to the surface is the recommended method.