Hi, I have a similar problem with an ancestor of my husband called James Connor, he is with his wife and daughter in 1851 and is listed in the 1855 Manchester directory as a cabinet maker in the same street as he was living in 1851. Then he just disappears.
No trace of the family in 1861, although there is a child of the correct age, initials only given, living at a Catholic Convent near to where the family were living in 1851. She married in 1867 aged 15, even though she said she was 18! His wife gave birth to an illegitimate child in 1862 and thanks to a Rootschatter, she was shown as paying rent at the address she was living at the time in from 1864-1868. She died in 1868.
There are so many James Connors in the Manchester area who died from 1855 onwards, but I can't get all the death certificates. The other thing is that his younger brother also disappeared around the same time, so I wonder if they both went back to Dublin where they were born. Their own father re-married in 1857 in Liverpool with all the Rites and Ceremonies of the Catholic Church, so you would assume his first wife had died. However, I wonder, as I can't find a death for her, if she and her 2 sons just up and left for Ireland.
I wonder if this was a common thing that Irish people didn't find England (Manchester and Liverpool) as good as they expected and just went back home? Could be what happened to your Thomas Logan.