Is it safe to update my modded 3dsxl?

I have an original 3dsxl that I’ve had modified for YEARS, I did the mod a really long time ago, and one of the only things that was driven into kid me’s brain while I was doing the mod was “DO NOT UPDATE”! So for years I have abstained, I see the popup every time I boot up my console and every time I hit no, I close out of apps that claim cannot be used since I’m not updated, life is great… but.. to be honest, it’s annoying. Very very annoying. The popup you get at startup has finally gotten to me. Is there a way to update my 3ds without bricking my console or having my mods get nuked? If not is there a way to get rid of the popup?