Last Easter, Mountbatten-Windsor, Ferguson and their daughters were all at the Windsor service, which is seen as a family event rather than an official engagement.
But since then Mountbatten-Windsor has been arrested on suspicion of misconduct in public office and has moved to Sandringham, Norfolk.
He no longer lives with his ex-wife, who also left the couple’s former home at Royal Lodge in Windsor.
Mountbatten-Windsor and his family have been engulfed by the Epstein scandal, with continuing questions about links to the US sex offender.
A US lawmaker, Congressman Suhas Subramanyam, last week asked Ferguson to testify about her ties to Jeffrey Epstein.
Mountbatten-Windsor has denied any wrongdoing from his connections with Epstein.
Earlier this month, Princess Eugenie stepped down as patron of charity Anti-Slavery International, a role she had held for seven years.