Never had a problem with devmenu. In fact, it's the only one that seems to handle DLC properly, even though others don't even complain or give errors... the DLC just doesn't work when installing them. And which version of FBI are you using? It must be old, because a file from CDN (such as Eshop or something that was created with 3dnus) shouldn't refuse to install for any reason. If the version is the same or older, FBI should ask you if you want to delete it or not to reinstall it. 1.4.16 is broken on N3ds right now, but 1.4.15 should be fine (although a bit quirky with deleting files during install... you just have to say yes delete it, then try installing again.)
If you're only installing a single file, or even just a couple, using sysupdater is pointless. Just use FBI.