Hmm, I was under the impression that an upgrade would "correctly" retain most (if not all) prior settings (printer settings are typically the only ones that might need to be reset). Myself, with my last two "moves" of the Mac OS (ie, from OS 10.9.5 to OS 10.10.1, and then from OS 10.10.5 to OS 10.11.1), I first backed everything up to an external drive, then Erased and Formatted my internal SSD, then did a clean installation of the new OS, and finally, via Migration Assistant, "migrated"/copied all the "needed" stuff from my backup. (Of course, I first made sure that I had either upgraded any third party software I have, or obtained the upgrades). Except for resetting the printer settings, everything else worked fine, including network/internet settings. I did all that for both of my Macs.
I will, most likely, do the same thing when the next new Mac OS comes out. But, for your issue, I am at a loss. Maybe someone else can chime in.
I hope you can get it resolved. I understand how frustrating it must be. One would think it would be simple!
I forgot to mention one other thing, although it will most likely not help you out immediately. Last week. Apple released a new version of El Capitan, OS 10.11.4. If you have not upgraded yet, you might want to consider doing that. I actually posted a thread about that, and the various "upgrade" options, on this site. Here is the link to that post:
https://www.mac-help.com/threads/new-version-of-el-capitan-os-10-11-4.221906/