You don't need to reset your switch to do that mate. IN FACT, reseting would not help at all, AFAIK because installing your cfw on your sysnad will leave trace data that NIntendo can collect through telemetry. If you are going homebrew a switch you intend to take to use on online play than you need to make a emuMMC. For homebrewing your switch, making the emuMMC and other misc. things you may want to check this guide, which atm is the most up to date.
The problem IMO would be if Nintendo would consider the modification of your pokemon save game a banable offence once you decide to sync with their online services in sysnand (After importing your emuMMC save to sysnand of course). There have been reports of modded or tampered saves eliciting bans, however again it seem your mileage may vary as Nintendo can be very random with their ban waves.