Residents in shared zone areas were assured they will be able to choose which school their children attend.
However, some living in the sought-after "double Grammar zone" believed it might be a first step to their eventual exclusion from EGGS and AGS, because of roll pressure on the two schools.
Submissions cited proximity issues and the desire for children to attend a single-sex school, and concern about the value of property was also a factor.
Last year the Herald reported that a Mt Eden home just 750m outside the grammar zones went for $516,000 less than a similar house up the road that was within zone.
Act Party Epsom candidate David Seymour set-up a petition against the One Tree Hill proposal after fielding "a stream of phone calls and emails".
Lobbyist and local resident and Matthew Hooton also protested against what he said was unsatisfactory consultation, and with other parents briefed law firm Russell McVeagh.
One Tree Hill College has now made the decision to withdraw any proposed overlap of the grammar zones.
The proposed Selwyn College zone will also be amended so it does not overlap with the two neighbouring schools.
One Tree Hill College said it wanted to remain focussed on the education of its students and not be drawn into "political manoeuvring" around enrolment zones in central Auckland.
"This is a success story of another New Zealand school doing extremely well and achieving excellent outcomes for our youth," principal Nick Coughlan said.
"It is not about what Auckland Grammar School and Epsom Girls Grammar may, or may not do, in terms of changing their zones.
"That is a decision for their respective boards of trustees. One Tree Hill College were simply proposing an enrolment zone to meet Ministry of Education guidelines."
That included the need to not divide areas and homes around contributing schools.
The college received about 150 submissions, the vast majority of which were from those opposed to the overlap with the grammar zones.
Mr Coughlan said the most who were opposed also recognised the college's success, and he wanted to acknowledge them. A handful were not so measured, however.
"There were certainly one or two who went full quid, for want of a better term."
Parent Jo Thomson, 48, has one child at EGGS and another due to start in the coming years, as well as a son at Auckland Grammar.
Mrs Thomson, a careers counsellor at Avondale College, said her submission objected to the uncertainty created by the shared grammar zones, as well as proximity issues.
However, she said it was a shame that the issue had detracted from One Tree Hill College's success story.
"People can get very protective of their little patch, I suppose...I recognise why it has to be done. But at the same time I live in that area because of where I want my children to go, so I don't really want that uncertainty."
Mr Coughlan said there were a number of families living in the grammar zones who sent their children to One Tree Hill College and other schools. They would now need to do so under out-of-zone regulations.
The college's roll has increased from 700 to 1000 in five years. The proposed zone has been drawn-up to ensure all locals can have their children attend.
The new proposal continues to overlap with zones for Onehunga High School, Selwyn College, Otahuhu College, Edgewater College and Glendowie College.
