Did this file start out as Excel file way back when? I do not have any old native Numbers files with me at the moment to play with but I do know that imported Excel files often have outlines around charts that cannot easily be removed and all new charts made in Numbers will have the same Excel-like formatting. I just now created an Excel file with a line chart and pie chart and imported that file into Numbers. There is an outline around each chart with no setting that I find to remove it, spaces between the pie wedges with no setting that removes them, and all new charts I make look just like those ones.
All is not lost, though, if you need to use your original file. Although this is an imperfect solution, it seems to work. Create a new Numbers document with a small table and the charts you want, formatted the way you want to see them. The data in the table can be gibberish, the chart styles are what we want out of this. Copy the charts and paste them into your other file. Then, for each, Copy Style then Paste Style onto the charts that are not formatted properly. Those charts should now have the correct Numbers formatting.
I say it is an imperfect solution because new charts will be created with the Excel-like formatting. Personally, when I have problems like this with an imported Excel file, I use your other solution of starting over with a fresh new Numbers document.