Ellen
Another problem with this simple story is that there were two Ellen Dooley's in the workhouse at Parsonstown in 1849. The workhouse register records the discharge of one Ellen Dooley in April 1849 and another in August. We also know that two Ellen Dooleys came to Australia as part of the Earl Grey scheme. One arrived on the John Knox in January 1850, the other on the Tippoo Saib that July. According to the immigration records, Ellen Dooley per John Knox came from Dublin. Taken at face value, there are now three Ellen Dooleys, two from Birr and one from Dublin. But it's equally plausible that the girl on the John Knox came from the Birr district via Dublin.
We know that one Ellen Dooley married John Flynn from Tipperary in a Roman Catholic Service in Dapto, to the south of Sydney, in 1851. We know that the same woman married John Cunningham in 1885. because, when she died in 1898, the Dunwich Benevolent Asylum in North Stradbroke Island recorded that Ellen Dooley was known variously as Mrs Flynn or Mrs Cunningham. Moreover, we know that Mrs Cunningham was the same person as the immigrant on the Tippoo Saib, because her marriage certificate records both her parents' names and her place of birth and those details match the immigration records.
On the face of it, the documents seem to show that Ellen per Tippoo Saib left Eliza and Catherine in the Hunter Valley and followed John Flynn to Dapto where they married. Several children later, she followed him to Tenterfield in Northern New South Wales, where she produced several more children before marrying john Cunningham. It seems she committed bigamy: John Flynn was still alive and there are no records of a divorce.
Some Flynn descendants believe this story and on the strength of it have erected a plaque in the Tenterfield cemetery.
But...but...but....
We also know that another Ellen Dooley married John Murray in Uralla in 1856. We know that this Ellen was intimately connected to Eliza and Catherine. Eliza is a witness on the wedding certificate, and Catherine Cleary's obituary describes her as a sister of both Ellen and Pat, the two surviving siblings. At the very least, it seems an extraordinary coincidence. It's so unlikely that one would suppose it would form part of family lore among Mrs Murray's descendants, but no stories mention it. The most straightforward hypothesis is that the two Ellens from Birr both came to Australia, one on the Tippoo Saib and the other on the John Knox, where they became Mrs Flynn and Mrs Murray. Of course, if you believe that, you must explain how Ellen from Birr became Ellen from Dublin, with a different set of parents.
Another explanation is that Ellen arrived under her own steam before the Earl Grey scheme began. The cost of a passage being what it was, it seems unlikely.
Still, as I said at the top, all these stories are provisional. An alternative story for Mrs Murray would help. I was not able to find any Australian evidence for the existence of Ellen per John Knox after 1850, or any Irish evidence that Michael and Bridget had a daughter Ellen prior to 1830, when Catherine was born. Written material from her latter life in Australia might help too. Until such comes to life, it remains a bit of a mystery.