Mary died at 10 Charters Street in January 1867, at the address of her daughter, Isabella, who was the informant on her death certificate.
Have you found Isabella in 1861 to confirm she wasn't living with her? Was she married or single at the time (Isabella)
Or one of the other children
Haven't been able to find Isabella either, unfortunately. She married John Cassidy in 1852:
22 August 1852: Liverpool, St. Peter:
John Cassidy, full, bachelor, [?] founder, Thomas St, Patrick Cassidy, baker
Isabella McGowan, full, spinster, -, Vauxhall Rd., John McGowan, tailor
Witnesses: James Fearon, Margaret McCormick
She married William Knowles in 1862, and appears on every census after that, until she dies in 1906, but I haven't found her in 1861.
24 September 1863: Liverpool, St. Nicholas:
William Knowles, full, bachelor, caster, Northampton [?] st., James Knowles, cart owner
Isabella Cassidy, full, widow, -, Arlington St., John McGowan, tailor
Witnesses: Thomas Robbins, Mary Dawson.
As for their other children, I have John and Mary (not Margaret, or Catherine) on the 1861 census, and I think I only found her with help from roots chat. There are some errors with this, the ages of her children are off, but the order is correct. I have her husbands death certificate in Freemasons Row in 1859, so, despite the errors, this is the right family.
1861: 49 Freemasons Row:
Margaret McGoverin, Head, Widow, 40, -, Liverpool
John do, Son, Unmarried, 20, carter, Liverpool
Lawrence do, Son, Unmarried 15, -, Liverpool
Martin do, Son, Unmarried, 12, -, Liverpool
Peter do, Son, Unmarried, 9, -, Liverpool
1861: 6 [?] St.
John McGowen, Head, Married, 34, Confectioner and broom maker, Liverpool
Ellen do, Wife, married, 27, -, Liverpool
Mary Ellen do, daughter, -, 16 months, -, Liverpool
Their marriage records:
16 December 1845, Liverpool St. Nicholas:
Martin McGovern, full, widower, porter, Midghall street, Thomas McGovern, weaver
Mary McGowan, full, spinster, -, same address, John McGowan, tailor
Witnesses: John Bannan, Alis T'Enney
15 August 1859, Liverpool St. Nicholas:
John McGowan, full, bachelor, broom maker, Gildarts Gardens, John McGowan, tailor
Ellen Mayman, full, spinster, -, Gildarts Gardens, John Mayman, broom maker
Witnesses: James Eaton, Mary Eaton.
Margaret also got married, but I haven't found her apperance on the 1861 census either.
17 July 1853: Liverpool, St. Peter:
James Fearon, minor, bachelor, cooper, Park Lane, Richard Fearon, cooper
Margaret McGowan, minor, spinster, Marlborough Street, James McGowan, Porter
Witnesses: Edward Brownhill, Ellen Brownhill.
Isabella and Margaret live together at the time of the 1901 census, both widows by then.
In summary:
Mary nee Johnson, - missing 1861 census:
Catherine McGowan, - nothing after 1841 census
Mary McGowan, becomes McGovern, all census returns, dies in 1895
John McGowan, all census returns, dies in 1866
Isabella McGowan, becomes Cassidy, then Knowles, all census except 1861, dies in 1906
Margaret McGowan, becomes Fearon, all census except 1861, dies in 1913
Any help anyone can provide, or even points in the right direction helps, many thanks!