After the Yorkist forces lost the Battle of Stoke on 16th June 1487, and many of them died, Francis`s whereabouts are unknown. Sources written some decades, and in one case even nearly a century, after the event sometimes claimed that he was last seen swimming on horseback over the river Trent, but even that cannot be ascertained. All that was said contemporarily is that he was "discomfited and fled". His fate afterwards is up for debate.
Even at the time, those closest to him did not know where he had gone, as can be seen from a letter his mother-in-law Alice FitzHugh wrote to John Paston some eight months after the battle, in which she mentions that her daughter Anne, Francis`s wife, has so far been unsuccessful in finding out her husband`s whereabouts. The full text of the letter is this:
"To my right trusty and welbeloved son, Sir John Paston, be this delyvered.
Jon Paston, I recommaunde me to you in my moste hertely maner. And wher I understande be my doghter Lovell, ye desyre to know whedir I woll have the bargane ye made for me in Norwich or nay, and if I wol, I moste content therefor now in merks. Son, in good faith it is so, I shal receyve no mony of the revenowse of my lyvelod before Mydsommer, and also I have payd accordyng to my promise to Sir William Cabell a great payment, the which ye knoww wel was due to be payde, so that I can not be of power to content therfore, for the which I am right sory, for I know well I shall never have such a bargane.
Also my doghtyr Lovell makith great sute and labour for my sone hir husband. Sie Edwarde Franke hath bene in the North to inquire for hym; he is comyn againe and cane nought understonde wher he is. Wherfore her benevolers willith her to continue his suit and labour, and so I can not departe nor leve hir as ye know well; and if I might be there, I wold be full glad, as knowith our Lorde God, Whoo have you in his blissid kepynge.
From London, the xxiiiith day of February.
Your loving moder, Alise, Lady FitzHugh."
This letter, though on the face of it fairly straightforward, has been interpreted variously over the years. Since the year it was written is not given, even that has been disputed. James Gairdner, notably, argued that the year had to be 1486, since there was no knowledge of Francis after 1487. However, this is almost definitely incorrect. For one, Alice addressed John Paston as Sir John, which given that he was only knighted after the Battle of Stoke, means it cannot have been written before 1487. Curiously, Gairdner mentions this but dismisses the address as a mistake, without explaining further why he thinks so.
It is not, however, just the address that shows the year it was written has to be 1488. In 1486, the year Gairdner dates the letter to, Francis`s whereabouts in sanctuary in Colchester were no secret. Moreover, Edward Franke was one of Francis`s co-conspirators in 1486, and would not have to have been sent by Anne Lovell to find him. It is quite clear, therefore, that the letter was written in 1488.
This is quite interesting in itself, as Edward Franke was himself a traitor at that point, and associating with him could have been dangerous to her. However, it seems that neither she nor her mother were afraid of any possible consequences of this.
It is also interesting to note that Anne Lovell apparently had several "benevolers" who supported her in this and were in fact urging her to further try and "continue her suit and labour", arguing she was a popular woman who even in less than good circumstances, as a vanished traitor`s wife, was not abandoned or even simply suffered by her social circle.
The exact nature of her "suit and labour" has equally been disputed over the years. The word "suit" and the fact that at the time of her mother writing this letter, she appears to have been in London, has led some people to argue that she was trying to secure a pardon for her husband. However, this seems a bit unlikely, as Francis had already rejected a pardon in 1485, and none of his actions since then give any indication he had changed his mind at some point. Given that Anne did not know where he was, he could also not have told her he had done so, so that it seems unlikely Anne was trying to secure him a pardon which would avail to nothing.
Moreover, given that Francis had at that point been responsible for two rebellions, one kidnap attempt and one assassination attempt on Henry VII, the likelihood of him being granted a pardon would have been negligible, even without him having already rejected one.
Moreover, her trying to have her husband pardoned does not make sense of Alice`s statements in the text, as she explicitly says because Edward Franke had not found Francis, Anne`s supporters were encouraging her to continue. If she had tried to get him pardoned, she would maybe have tried to continue doing so despite Francis not having been found, but not because of it. The only way this could make sense would be if she tried to get a pardon for herself and hoped to dissociate herself from Francis, but this directly contradicts both her actions and Alice`s words. If she had wanted to dissociate herself from him, Alice would never have said she was doing it for her husband, and Anne would not have associated with traitors, putting herself in some danger, to find him.
Instead, Anne`s suit and labour almost certainly seems to be refering to her trying to find Francis. Why and what she hoped would happen if she found out his whereabouts, there is no hint given in the letter. What is notable, however, is that Alice clearly supported her and does not display any grudges towards Francis and the fact his actions had put her daughter in a bad position. On the other hand, she explicitly refered to him as her son, even when "my daughter`s husband" would have sufficed. She also refered to Anne not as "my daughter Anne" but as the conventional "my daughter Lovell", suggesting neither of them wished to stop her being associated with him.
Finally, it is interesting to note that Alice and Anne clearly had a good relationship, in which Alice supported Anne and her choices and wished to be there for her.
If they ever found out what happened to Francis, we do not know. Anne took a religious vow sometime between the time the letter was written and December 1489, which could indicate she had found out he was dead, but could equally mean she had given up hope to ever find him again. It is, however, notable, that she was still only 29 in December 1489, yet had still chosen to take this vow, which would prevent her from ever marrying again and having children.
Sadly, there is no indication what Alice thought of it and if their relationship stayed as good as it appears to be in February 1488.