The site now houses one of Wendy's rivals, Carl's Jr, as well as a Subway restaurant, a TAB and a liquor shop. A Mobil service station previously occupied much of this land.
Wendy's was not given a copy of the trust's application for resource consent and claimed the changes had adversely affected its business.
The fast food chain's owner went to the High Court in 2014, arguing the council's decision to not notify it of the application was unlawful.
It wanted the consent quashed but this was refused by Justice Mary Peters.
Wendy's then challenged that decision in the Court of Appeal and was successful just before Christmas.
Justices John Wild, John Fogarty and Jillian Mallon said Wendy's application succeeded "on proof of an error of law".
The council, in light of the decision, has to reconsider whether or not Wendy's owner was affected by the changes at the site.
If the council deems Wendy's has suffered more than just minor adverse effects, then the local government body must reconsider its decision to grant resource consent.
Wendy's owner, Wendco (NZ), was awarded costs.