I hadn't thought of Lydia joining a non-conformist church, I imagined something far more sinful(!)but that's possibly what happened. There was a Baptist and a Congregational church in Yarmouth at the time, or possibly she joined the Quakers as you suggested, Bristolian.
Whichever chuch it was either she, or her daughter Deborah,obviously changed her mind when it came to Anne's baptism.
I've checked Ancestry, Freereg and Family Search, but I can find no further reference to either Anne or Deborah.
Lydia's husband Christopher left a will, the NRO have the probate records, but I don't have any details. Presumably Lydia was sufficiently provided for so she could have supported Deborah and Anne.
Interestingly, Christopher seems to have been fairly litiginous. There are references to his being a plaintiff in a case concerning property in Oby, where he was rector, in 1654 and to another case with his brother John, where they were plaintiffs in a case, again concerning property, this time in Norwich. These are listed in the National Archives catalogue, but again, I don't have any details.