I was glancing at my copy of New England Marriages Prior to 1700 by Clarence Almon Torrey (the reprint, 1992) and on p. 121 I noticed under my ancestor Thomas Burnham who married Lydia Pengry (daughter of Moses and Lydia (Clements) Pengry) on 13 February 1665/6 at Ipswich, Mass. [Vital Records of Ipswich, Massachusetts to the end of the Year 1849 (Essex Institute, Salem, MA, 1910), II:73], that he "was the nephew of Robert Allen." This was completely new news to me.
Luckily I live in Boston so I went to the NEHGS Library where the original Torrey in all of its splendor resides. Clarence Torrey hand wrote notes for every marriage in New England prior to 1700 and his work, some eleven volumes is a must-use for New England genealogy. I looked up Thomas Burnham and certainly it says "nephew of Robert Allen" and gave the cite: Allen (1890) 20. This generally means there was an Allen genealogy published in 1890 and the relationship is noted on p. 20. Since Torrey worked at the NEHGS, he exclusively used that collection and whatever he cited is generally on the shelves. Not this time. In fact, in the listing of works cited there appears an ominous note: Allen (1890) not identified.
So what to do? I assume he meant Robert Allyn who was in Salem to 1651 before moving to New London and then Norwich, Conn. However, there is also a Robert Allen in Kittery in the 17th century. Since Robert Allyn died prior to 1683, the relationship of uncle must be in a document prior to that. And the relationship must come through his wife Sarah (---). Thomas Burnham was the son of Thomas and Mary (Lawrence) Burnham and his wife Lydia is noted above. No Allens. We can further pare this down. Mary Lawrence had no siblings named Sarah. See: Mary Walton Ferris, Dawes-Gates Ancestral Lines vol. 1 (1943) and vol. 2 (1931); The Genealogist 10 (1989):3-30; and The Great Migration Immigrants to New England 1634-5 by Robert Charles Anderson, (Boston, MA, NEHGS, 2005) Volume IV. Lydia Clements had a sister Sarah, but she married Abraham Morrill and Thomas Mudgett. Robert Clements left a very explicit will [Essex County Probate #5604] See: Ancestry of Charles Stinson Pillsbury & John Sargent Pillsbury by Mary Lovering Holman (2 vols., 1938) and Ancestors and Descendants of Robert Clements by P.W. Clement (1927). It seems unlikely that Sarah would be a Burnham since Robert Andrews mentions his kinsmen, John, Robert, and Thomas Burnham, in his will of 1 March 1643/4 (Essex County Probate 1:27-28]. Surely if Sarah were also a sibling and living in Salem, she would have been grouped in as well. That leaves Moses Pengry, whose origins are unknown as a possible brother. Moses was born ca. 1610 and deposed with his age eight times in Essex Court records.
Robert Allyn appears in Donald Lines Jacobus's work The Granberry Family and Allied Families (1945), but doesn't mention this relationship. So, we have a mystery. One man who live in Ipswich was possibly called nephew by a man who lived in Salem, New London, and Norwich. What type of record was it? A deed? A court case? The Essex court cases are published to 1686, three years more than Allyn lived. A mystery.