I have no delusions that this article will not be confusing with all the Edwards and Johns, and it’s because of that I’ve included this list of players to help you differentiate between them:
Edward Seymour/Sir Edward – Later Duke of Somerset, married both Katherine Fillol and Anne Stanhope.
Sir John Seymour – Father of Edward Seymour, later Somerset.
John Seymour – First son born to Katherine Fillol and ?
Edward Seymour/Lord Edward – Son of Edward Seymour and Katherine Fillol
Katherine Fillol – First wife of Edward Seymour/Sir Edward
Anne Stanhope – Second wife of Edward Seymour/Sir Edward
In 1514, Edward Seymour (age 14) wed Katherine Fillol, and until Edward reached 21 the couple were to live at Wolf Hall, and would be fully provided for. That same year, Edward was part of Princess Mary’s (sister to Henry, not daughter) household. He was also enfant d’honneur (child of honor) at her marriage to Louis XII of France in October 1514.
The Mystery Begins
Surrounding their story is much confusion, when it comes to Katherine and Edward. Let’s begin with her age: The History of Parliament states that Fillol was in her twentieth year when her father settled his estates, in 1527. If “twentieth year” meant she was twenty, then she was born about 1507 and would have only been seven years old at the time of her marriage to Edward Seymour. An age that was no longer lawful to marry. If they meant she was in her twenties, then that opens it up much wider, and she could have been the same age of Edward.
When we examine the couples marriage agreement, it becomes clear that something caused both of their father’s to agree on a specific term. That if Edward would ‘disagree with the marriage’ within three years, Sir John Seymour would pay 200 marks for Katherine’s next dowry. Three years after their marriage would have been 1517. If Katherine was born in 1507 (unlikely), her young age may explain the verbiage in their marriage contract, but does not explain why she would have been eleven years old when she had her first child. Marriagable age for girls was twelve, with age of consent being fourteen (a standard that Margaret Beaufort helped establish).
Rumors About Paternity
In 1518  , the couple welcomed a son, and called him John. Sometime after the birth of their second son, Edward, rumors abound that Sir John Seymour (Edward’s father) was in fact the biological father of John. Some have stated they think it possible since Edward had been at university, and Katherine was at Wolf Hall without him. While facts are obscured by gossip, it is clear that Katherine Fillol ended up in a nunnery. It is also clear that she (her husband and heirs) was disinherited as co-heir of her father’s estate.
Something that has been made clear to me is that it wasn’t only Katherine (as co-heir) who was disinherited, but also her sister and husband. Sir William Fillol took every precaution to ensure they never received their inheritance. But in 1530, his will was set aside by an Act of Parliament on account of his ‘having many sundry fantasies in his latter days’. Katherine and her sister then shared their rightful inheritance. But what caused the fall out with their father? Had he merely gone mad, or was he provoked?
In 1674, Peter Heylyn is the first to mention the story of Edward Seymour in France. While in service to the King in France, Edward had acquainted himself with a seer who foresaw an event between his wife Katherine, and an unnamed gentleman in a “familiar posture“. Heylyn also believed that Edward Seymour’s eldest son by Katherine was Edward, not John, so from the start we have incorrect information. 
Horace Walpole also mentioned how a handwritten note was spotted in the margin of Vincent’s Baronage in the College of Arms, ‘a book of great authority’ (published in the 17th century), that Katherine Fillol was ‘repudiata quia pater ejus post nuptias, eam cognovit’.  Roughly translated to: divorced because his father after the wedding, she knew. Walpole lived in the 18th century, and likely had access to both works.
In 1527, when Sir William Fillol disinherited his daughters (and co-heiresses) in his will, he said:
First my very will and intencion for many dyverse Causes and Considerations me movyng that nether my daughter dame Kateryn Seymour nor hir heires of hir boody ne Sir Edward Seymour hir husbonde in any wyse have any parts or parcell of my said manors londes tenementes and other premises.’ All she was to receive was 40 annually for life ‘as longe as shee shall lyve vertuously and abidei n some honest house of Relegion of wymen.’
Yf my seid doughter do not lyve vertuously and abide in some honest house of religion of wymen to the pleasing of God, then I will that my said doughter have no parcell of the said 40, but the said executors do dispose thereof towards the performance of my testament and last will and other good deed of charitie.’ 
This would indicate that in 1527, when he made those stipulations, that Katherine was already in a convent, or nunnery. Where were her sons? Did they stay at Wolf Hall with their father? Or is historian David Loades (The Seymours of Wolf Hall) correct in his assumption that they stayed with their mother?
At some point, prior to March 1535, Katherine Fillol died. Sir Edward Seymour married Anne Stanhope on 9 March 1535. Anne Stanhope had made sure her husband only recognized the children she had by him, excluding the sons by Fillol. In 1540 she got her way. An Act of Parliament was passed that disinherited John. The younger son, Edward, was spared from being the paternity question, but he would not inherit his father’s titles and land – that would go to any half-brothers by his father’s second wife, Anne Stanhope. The only hope he Edward could have imagined was if his father had no surviving sons, then he would rightfully inherit everything.
The Trail Goes Cold
After Sir William Fillol made mention of his grandsons (‘hir heires‘) in his will, the trail goes cold on John Seymour for about two decades. There is no indication of a wardship for either John or his brother Edward, and David Loades believes that means they were with their mother until her death in 1535, and then their care reverted to their father.
Is it possible that they stayed at Wolf Hall with their grandparents while their father was at court? If, like Loades says, they had stayed with their mother in the nunnery, the loss of records and gap in time would be explained.
Downfall of Somerset and Fate of John
It seems that Sir Edward Seymour, Duke of Somerset still had a good relationship with both of his sons by Katherine Fillol. When Somerset was arrested and thrown in the Tower, so were his sons. The younger son, Edward, was soon released, but John did not have such fortune.
Sir Edward Seymour, Duke of Somerset, was executed on 10 October 1552. John, on the other hand, was left to languish in the Tower of London. In her well-known book The Seymour Family (1914), author A.A. Locke states that the name “John Seymour” was still inscribed on the wall of the Beauchamp or Cobham Towers. It is in the Tower of London that he spent the last months of his life, being nursed by women he did not know.
From the Tower of London, John Seymour petitioned for restoration to the lands which had belonged to his mother. It was in his prison that he learned the 1540 Act had been reversed. His mother’s estates had already been sold, but Parliament ordered that compensation should be made to her children. John would now be given the same amount of income that he would have received from his mother’s lands.
The manor of Maiden Bradley, excepting the land of Yarnfield and Baycliff, was ‘awarede to John Seymour‘, with the added provision that, ‘as the manor was considered more valuable than the properties in lieu of which it was given, the estimated difference should be yearly paid to the children of Anne Stanhope, to whom the manor was secured.” 
But it turns out that his younger brother Lord Edward was the one who would benefit most. In his will, John Seymour was generous, and left legacies to the two women who had nursed him. In addition to that, he made his brother his executor, since he had never married or had children.
Also I make my brother Sir Edward Seymour the elder, my full executor, and I give him all my lands and goods that is bequeathed’.
Will of John Seymour
 History of Parliament, pg. 292-3. Link: (https://bit.ly/34oEmhq)
 Heylyn, Peter, Ecclesia restaurata; or, The history of the reformation of the Church of England. (1674), pg. 3. Link: (https://bit.ly/2HtuXvY)
 The Letters of Horace Walpole, Earl of Orford Edited by Peter Cunningham, Volume 2. (1877) pg. 204. Link: (https://bit.ly/2TklEBa)
 Inquisitions Post Mortem c. 142/46/25, Sir William Fillol, 19 Hen. VIII. P.R.O.
 House of Commons Journal Volume 1: 03 March 1552 –Journal of the House of Commons: Volume 1, 1547-1629. Originally published by His Majesty’s Stationery Office, London, 1802. ‘House of Commons Journal Volume 1: 03 March 1552’, in Journal of the House of Commons: Volume 1, 1547-1629 (London, 1802), pg. 19. Link: (British History Online http://www.british-history.ac.uk/commons-jrnl/vol1/p19j) [accessed 23 September 2020].
Diary of Henry Machyn, Citizen and Merchant-taylor of London, from A.D. 1550 to A.D. 1563
Heylyn, Peter, Ecclesia restaurata; or, The history of the reformation of the Church of England. (1674)
History of Parliament
House of Commons Journal Volume 1: 03 March 1552
Inquisitions Post Mortem
Loades, David, The Seymours of Wolf Hall.
Locke, A.A., The Seymour Family (1914)
The National Archives (Kew)
Seymour, William, Ordeal by Ambition.
Scard, Margaret, Edward Seymour – Lord Protector.