I thought you might be interested in a bit of up dating on the Thomas saga. Another Thomas seeker after history has got the death certificate for 1853 for Harriet Thomas and it's not her. The birth certificates for two of the children at the 1849 baptism (Charles and Augusta) both show Sarah Cooper as the mother so we have to go forward on the basis that she was the actual mother of at least the last 4 children of Daniel Thomas. In trying to think about the marriage of Daniel and Sarah, there was clearly no inhibition about telling the government he and she were married on the birth certificates so the only conclusion I can reach is that Harriet Thomas was alive until the back of 1855 because she was the just impediment to the marriage. Now whether she had done a runner or was confined to an asylum I can't find any evidence for either although instinct says the latter.
What confuses the matter further is that a Harriet Thomas who gave birth to a Harriet Thomas in 1826, died in the workhouse in 1829. There are also 2 baptisms of a Charles Joseph Thomas, one illegitimate in 1824.; one to the child of the same name born of Harriet and Daniel Thomas in 1825 - same church same minister.
The final confusion is that the Thomas family, whoever was the mother, are completely absent from the 1841 census. Sarah Cooper/ Thomas is similarly not in the 1851 census that I can find.
There's the makings of a victorian novel here of dual identities. As you said it's a mystery.