Just what we need! More Johns and Emanuels! If as you say Ann Miller was made Trustee of her husband's estate, she may have continued to manage the farm, perhaps together with his son, also Emanuel, and perhaps his other children. This is a reasonable assumption.
I went to the census records to check. In 1860, an Emanuel Custer lived in District 2, Allegany, MD with his wife, Mary. He was 21 (b. 1839) and she was 19, married within the year. This could have been a grandson of Emanuel-the-Elder, and there may have been a Deed filed transferring part of the farm to them. I'd say the farm continued after the farmer perished.At some point, Ann sold off part of the land.
In the 1850 and 1860 census, the only other Emanuel Custer family lived in Ohio - that of Emanuel and Maria Kirkpatrick and children Nevin, Thomas, Boston and Margaret.