What skin illness would cause long term heel lesions with a strong smell?

Bacterial infection. Heel lesions with small holes in the skin are caused by a kind of strep called pitted keratolysis. It is caused by excessive sweating which allows the bacteria to over grow. Decrease sweating with antiperspirant at night on feet, insole to absorb excessive sweat and topical Erythromycin as used for acne.
Ulcerations ? I don't know what is meant by long term as well as "lesions", but a strong smell almost always means a bacterial infection. The worst case scenario is chronic infected ulcers secondary to a more systemic disease such as diabetes. It is interesting, no mention of pain was made. This may indicate a neuropathic problem. I recommend you seek evaluation by a competent specialist. Sooner than later.
Fungal infection. Fungal infection can create strong smell. From holistic perspective if kidney energy not in harmony this would occur.