I reviewed the various suggestions, and the reference to death records in Lisburn comes closest to a match. That entry describes an Isabella Phoenix, with death recorded Jan-Mar 1896 in Lisburn. It gives an age of 59 years and an estimated birth year of 1837. Maiden name is blank.
The Isabella Ph....... letter mentions an "Elizabeth" that was planning to send "sonny" a new dress, but there was not enough time now as the John Kelly family was leaving Ireland forever. The child is interpreted as being John's 10 month-old son in 1892. Isabella knew that John's mother had just died, but no mention that his father had died in 1890. No way of finding out who Elizabeth was, but it is written as if they would know her. Maybe just a room-mate.
So we have an Isabella Kelly who arrived at NPC in 1863, was a witness to Maria Kelly's marriage in 1865, and may be the Isabella Kelly who gave birth to Jane Kelly, 17 June 1865 in Bellaghy, Rasharkin Parish District of Clough, Union of Ballymena, with no father identified. Then she disappears as a Kelly. We know she was not the Isabella who married a Phenix in 1858, because then she could not have been a Kelly in 1863 or 1865.
If the death record is of our Isabella, then it suggests she either died alone, or those with her knew nothing of her family background. She may have made up her last name. A sad end, whoever she might have been.