If you already have an up-to-date emunand, then formatting it has nothing to do with anything. Your problem is something to do with booting it. You've clearly misplaced some items in your SD card somewhere.
Followed a step by step video with all the files being shown and I was checking them with mine , but the guy on the video was able to install rxtools without a problem (he didn't get that X at the first set up so I know there's something wrong hahaha
But I'd still like to know , is it safe to just format my 3ds and format the Emunand (using GW launcher.dat) ?