To paint or not to paint stone bay window?

First of all you will need to identify the type of stone. This will generally be either a sandstone, limestone or granite with many types of each throughout Britain. Depending on the type of stone there are different repair techniques. If the stone is limestone, maybe Portland stone, for example. I would recommend a mixture of mortar repairs and piecing in of stone. A mortar repair for limestone is a lime based repair mix made to colour match the stone. Once the lime mortar is cured its chemical composition is the same as the limestone substrate and therefore behaves much the same as the limestone. Piecing in of stone involves cutting out damaged areas of the stone and "indenting" or "piecing in" matching stone to the original stone cill. I would advise not to repaint the stone as this creates an impermeable and non porous barrier. This prevents moisture from escaping the building and can be very detrimental to the stone in the long term. Photos would really help to provide more specific advice but I would advise getting a qualified stone mason with experience of building conservation to look at the job. You will end up with a much more sensitive and aesthetically pleasing job. Hope this helps you understand the basic principles of stone repairs