The reason your sand gets stinky is anaerobic bacteria in the soil. This is very common with heavy /clay soil and the sand layer reduces the oxygen in the soil even more. Tilling in (non renewable) peat moss or (renewable) coco coir or a few times a year will help, especially if you can dry out the soil. Tilling in the sand will make it worse. You can relocate the coop to higher ground or use mulch instead of sand. We are using crushed filbert (nut) shells this year.
We dug a 18" deep trench around the perimeter of our shed and filled it with rocks and gravel, but it only takes a few years to the silt to return and soil in the area is starting to be saturated in the winter again.
We used a product (enzyme?) to treat the stinky soil where water dumps out of our sump pump into the yard and it worked but I can't find it on the internet now., if I find it I will post the name later.