Mayor Alvin Brown's administration has pitched the structural alterations as a way for employees to be more efficient and rename some departments.
It was introduced in March, but put aside while City Council went into its in-depth budget review mid- to late-year.
Some of the more notable proposed changes affect public works, which would have distinct divisions charged with engineering and infrastructure, and the neighborhoods departments, which would serve in more of a regulatory compliance role
In several meetings over the past couple of months, a council group led by Vice President Clay Yarborough has reviewed the administration's plan, debated the merits of certain items and made changes as it has seen fit
It originally was charged with completing the task by the end of the year, but with the amount of information involved, council President Bill Gulliford extended the time until February.
"We have had some productive discussions," Yarborough said. "Hopefully we will be wrapping it up soon to get recommendations made to the final body."
He said his hope is a joint meeting in January could complete the work before sending it to the full council for deliberations and wrapped "at most within the first couple months of the year."
It's been a work in progress with some back-and-forth between the council and the Brown administration.
For instance, at the end of a meeting in November, council member Bill Bishop proposed the basics for his own organization chart, making some key changes to the administration's proposal.
Council member Richard Clark then proposed dropping the city's Military Affairs, Veterans & Disabled Services from a position that reports directly to the mayor to one housed within Parks, Recreation & Community Services.
That passed, but in a later meeting the military and veterans affairs portion was brought back, with the disabled services left in parks.
Council member Stephen Joost supported that move, saying it shows others outside the city how serious Jacksonville is when it comes to veterans services.
Regarding the top positions in the administration that report to the mayor, several council members also have bristled over a certain term.
"I don't like the word 'cabinet'," said John Crescimbeni. "I am tired of hearing that word … it sounds too much like Washington (D.C.) and I don't think anybody around here likes Washington (D.C). I think we are getting a little bit too big for our britches."
Clark and council member Matt Schellenberg also voiced their disdain for the term, with Clark saying the structure "doesn't work" and that the city should be separated into business and political units.
He also has pitched that the Office of Economic Development be housed under the city's Finance Department instead of as a direct mayoral report.
The idea of whether the organizational charts meant anything also was discussed — several council members said the mayor could talk to whomever he wanted.
Bishop called the process "nothing … but a bunch of lines on a piece of paper" and said the process is only as effective as the people who are in the "boxes," or leadership positions.
Yet, despite the debates, Yarborough said the end changes after a full review should mean a city that runs more efficiently and possibly cost savings.
"The more questions we ask the better," he said.
The second phase of the City's reorganization likely will come to an end in the next couple of months, almost a year after it was introduced.