How do you reply to a notification from Riot Games?

I assume you mean a boards notification? You can't, not directly to the moderator in the way you mean, at least. If you need to contest a removal or a boards ban you need to submit a Support Ticket.

If you just want to inquire on the rules of the boards to better understand the notification you can post on this board (please don't repost what got removed), or you can ask on the Moderation Discord; http://boards.na.leagueoflegends.com/en/c/miscellaneous/9RBNln7l-discord-verification

Thanks. And that also goes if I'm kinda ok with the deletion but not with the implication that I have done anything wrong+the threat of a ban?

you can go into discord and have a chat with the forum mods.

You can dispute a punishment if needed.

Alternately, just ask here. That's what this section is for. Just don't include the removed content. We have the ability to review your removals so can find that on our own.

My deleted post was in reaction to someone and I don't think that person would benefit from reading an elaborate analysis on the makings of my reaction. I'll try the discord when I have time, thanks.