I've had this happen maybe 4 times with Skyrim, but only Skyrim at that point. I kept getting a message saying "Software was closed as an error occurred" or something.  It hadn't happened in a while, but it did  tonight while playing Fire Emblem Warriors. Now I'm concerned. I thought it was only one piece of software, but I feel like it's the system now. 

Is there anything I could try to avoid this? Has anybody else had these issues?

I just don't want to lose hundreds of save data... I really cannot understand why they haven't had the option to move your data to another switch or attach it to your NNID.