I just setup A9LH and skipped the step in which you removed your EmuNAND because I would still like to use it alongside SysNAND.
For what reason? If Sysnand CFW was unsafe it wouldn't be in the guide.
If it's for Gateway then you can use 9.2 Emunand to boot into it.
Regardless CakesFW and AuReiNand let you boot into emunand.
To boot into emunand on AuReiNand hold R while turning on the 3DS.
To boot into emunand on CakesFW hold L while turning on your 3DS, go to select patches, then enable emunand.