Remove pretty much everything that's usually included in sigpatches archive file i.e.:
- folders es_patches, nfim_ctest and nim-prodinfo-blank-fix from the atmosphere/exefs_patches folder.
- folders fs_patches and loader_patches from the atmosphere/kip_patches folder.
- patches.ini file from the bootloader folder.
That should be it. Don't forget to reboot afterwards after you install the latest sys-patch (simply drag and drop).
In any case, I've just updated my CFW (firmware, Atmosphere, Hekate, sys-patch, MissionControl and a couple of other apps) and from what I can tell everything still works just fine. The only issue I run into was that my Switch rebooted on first boot right after the Switch logo. The second time it booted properly.