The Irishman had three children with his former wife Carolyn - equestrian artist Nichola, 34, former event rider and amateur showjumper Natasha, 31, and Harry, 22. He was also the father of jockey Toby Atkinson, 27, from one of several affairs during his marriage.
Miss Owen began working for Eddery at his training yard in 2009, six months after Carolyn walked out on him after 31 years of marriage, blaming his heavy drinking.
She reportedly became his partner around three months later and moved into his home at the 100-acre Musk Hill stud farm near Aylesbury, Buckinghamshire.
Eddery's daughters had an acrimonious relationship with Miss Owen and claimed they were not even told he was in hospital for five days before he died from a heart attack after a coronary blood clot.
Natasha put out an emotional statement on Instagram after Eddery died, saying she had not seen him for five years due to his drinking, although they spoke by phone.
The message said she last saw him when she brought him home from rehab in 2010 and he started drinking straight away.
Natasha, who is married to trainer David Dunsdon, added in her statement: "My siblings and his close friends did all we could to help him battle his illness, but we lost in the end."
Speaking about his will yesterday, she said: "I have put all my stuff about my dad behind me... It doesn't really bother me. It's his choice. I'm not upset about it because my dad was ill and I didn't see him as my dad any more."
Miss Owen, who still lives at Musk Hill, said she believed Eddery's daughter Nichola was contesting the will. She said Eddery had provided for his daughters for many years, but they had "walked out of his life because they just couldn't respect his decision to move on and be with someone he wanted to be with".
Miss Owen added: "They didn't like it and they used [his] drinking to excuse their own behaviour. He didn't turn his back on them at all."
She also revealed she and Eddery had been about to marry, but he died a month before the ceremony was due to take place.
Eddery's son Toby said he was "a bit disappointed" to inherit nothing but had no hard feelings.
Eddery gave up his jockey career in 2003 and set up his Musk Hill yard with 40 horses in 2005.
Additional reporting by Laura Molyneaux