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The city's transport committee agreed to retain the active travel measures on Lanark Road, along with the scheme on Silverknowes Drive, which was also controversial.
Transport convener Lesley Macinnes hailed the decision as a significant step in the transition from temporary schemes under Spaces for People towards the long-term benefits of more sustainable infrastructure.
She said: "It is of immense importance that we retain as much as we possibly can out of that enormous investment of Scottish Government funding which was given to this city and which we've used as wisely as we possibly can."
But Lib Dem councillor Kevin Lang highlighted problems with the consultation which the council ordered in June. After the online survey went live, residents complained one of the questions forced them to choose to one of the options, with no opportunity to say neither, before they could move on. The council had to change it and go back to those who had already completed the survey.
Councillor Lang said: "Lanark Road has always been one of the most contentious schemes. You would think the greatest possible care would be taken with the community survey the council asked for, but it was botched initially, had to change mid-way through and respondents had to be asked if they wanted to change their response.
"With the council having been clear that a decision should only be taken after a proper community survey, I feel it would be wrong to proceed on basis of what is seen to be a flawed consultation. Doing so would open is council to the clear risk of a legal challenge I fear."
Earlier, Professor Derryck Reid of campaign group South West Edinburgh in Motion told the committee it had received legal advice that a decision based on a flawed or misleading consultation would be challengeable.
He said the Lanark Road scheme had cost of up to £200,000 but had not increased cycling by a statistically significant amount, had had a negative impact on people with disabilities, had seen speeds increase, prioritised pedestrians below cyclists and did not have majority support from the community.
A representative from another campaign group SW20 backed the scheme and argued the council should be bolder.
"While Edinburgh is talking about whether there should be active travel schemes other cities have moved on to talking to their citizens about how they will deliver them. Comparable cities have bold visions about their future - Birmingham, Glasgow, Manchester are making these changes now."
Two pedestrian crossings will be added to the Lanark Road sheme at Hailes Gardens and Kingsknowe Park. And parking adjacent to Kingsknowe Park will be relocated from the west side of Lanark Road to the east side.
Tory group leader Iain Whyte welcomed the crossings but called for the rest of the scheme to be removed along with the Silverrknowes one.
"We've consulted residents but we’re not listening to them on either of these schemes.
"What we need is properly-designed, fully thought-out, properly-consulted schemes that take people with us.
"At the moment this is a scattergun approach across the city that is causing huge frustration."