Every now and then, the “Manage Playlists” function stop working. The Lakka logo appears and you are thrown back to the main menu. Having scanned my romsets manually and using refresh to update, this is an issue when this occurs. Deleting the playlists (via SSH or Samba) gets around this but I can’t figure out what causes this to occur. Does anyone have any ideas?
Guessing is very complicated. The convenient thing to do is to create a log record and publish it on github. This you should know, you are already an advanced user. 
Also keep in mind that modified, the system on your own or installed cores, will possibly fail.
Thanks for the suggestion alexb3d. Forget I already had a github account, so have logged the issue. Not sure what you mean by the last paragraph though.
I have read that you install/upgrade cores that are not supported, or make modifications, those things can affect the performance of Lakka.
Yes, I see what you mean. I have downloaded nigthly cores in the past which allowed me to run newly added games, etc. As you mentioned, these did cause issues so I now tend to stick with what has been issued with the release.
This has happened to me too on my Raspberry Pi and it is a RetroArch bug that I suspect appeared between 1.14 and 1.15, although I have not investigated it thoroughly.
It has nothing to do with custom cores, which I have always used.