Honestly I use CFW on my SYSnand only for checkpoint. My EmmuNand doesnt connect to Nintendo servers already for whatever I use it for. People say there is a risk when using CFW on your sysnand. And they are not wrong. We dont really know what Nintendo looks for or what they will look for in the future to ban people. But generally editing saves has been safe for a lot of people. As long as you are not doing illegal stuff on your sysnand and doing things like save editing you are generally safe. For now at least. I usually only boot cfw and inject the save then boot back into emmunand immediately without issue. In the end its your call, I just thought I would let you know what I know not that I am an expert or anything.
Hey idk if you still have this problem and I JUST hacked my switch. Got my 1st unpatched and molded it yesterday for pokemon. I've had the same problem. I tried to disable the emmunand and nothing. It worked 1 time but it was not the save I wanted and I was so frustrated trying to figure it out. And what I did was you have to save the file back to the sd card. Plug in the card edit your save and export it back in one go. I got use to doing it like I did on the 3ds where I kept a file on my desktop edited it then plugged in my card and updated it. So how I got it to work was plug in card and launch pkhex and have it so it auto pulls your save. Edit it then export it in one go. If you prefer to have a file on your desktop like I do then edit it first and then plug in your sd card boot a 2nd pkhex and drag and drop your new edits. Export your latest pkhex project back to the card and bam. I'm new to modding the switch so idk wtf I'm doing just thought I'd try and help.