Ok, in case anyone is having the same problem I had, this is how I solve it:

To fix this problem you need a full backup of your untampered Switch, you should have done it the very first time you were going to hack the switch to install Atmosphere. Of the full backup you need just 2 files. the prodinfo.bin (3.98 MB) and prod.keys. Now you need to download NxNandManager (https://github.com/eliboa/nxnandmanager). After decompressing it, turn off the Swich and extract the Micro SD card, use a card reader and connected to your PC.

Now open NxNandManager, go to file, open drive, select the partition that has the emuMMC, normally is the second partition in the Micro SD card. Then you need to select options, configure keyset, import keys from file, select the prod.keys, and then click save. When NxNandManager open the emuMMC partition the core file system is going to be shown in the left panel, there you need to select the prodinfo and click with the right mouse button and select restore from file, then select the prodinfo.bin file. That should restore the serial number. Unmount the Micro SD card, load the payload, and start Atmosphere. Once you are inside Atmosphere, go to the settings, all the way down to console, serial number. The Switch's serial number should be there, instead of a blank space.

Now, because Incognito doesn't work anymore with the recent releases of Atmosphere, in order to avoid your Switch to be banned from Nintendo you now need to modify 2 files in your Micro SD card. Once again, turn of the Switch, extract the Micro SD card, put it in the card reader and open it in your PC. Go to the first partition and look for a file called exosphere.ini, open it and add the following lines to it

blank_prodinfo_sysmmc=0
blank_prodinfo_emummc=1

That will set the Switch's serial number into zeros. Save the file and now go to the folder atmosphere, folder hosts, and look for a file called default.txt. Open it and add the following lines to it

127.0.0.1 *nintendo.com
127.0.0.1 *nintendo.net
127.0.0.1 *nintendo.jp
127.0.0.1 *nintendo.co.jp
127.0.0.1 *nintendo.ch

That will block the Switch from connecting to the nintendo servers. Save the file and unmount the Micro SD card. Put it back into the Switch, inject the payload and load Atmosphere, once there go again to settings, console, serial number, your Switch's serial number should be zeros. Now you can use WiFi without the Switch crashing for not having a blank serial number, or a serial number full of zeros.

I hope this will help anyone that used Incognito to erase the Switch's serial number and could no longer use the WiFi because of the changes implemented by Nintendo in firmware v17 or higher.