I think you need to “unlink” and start afresh.
I suspect the information re Joseph Patrick and St Michael’s parish etc you have stems from the military record of another Joseph Patrick. Details on FindMyPast. Clearly not the same man.
NB I noticed in the report of Herbert’s funeral that Eleanor went by Nellie, so need to remember that for 1901. (Not that it has helped me!)
I am presuming they were still HAMILTON in 1901, but have searched under both names.