Ran npm i --unsafe-perm node-red-node-sqlite@latest in the .node-red dir as user pi as suggested.
After lots of warnings.... it did the job. At that point, 2 other nodes needed updating so I did those then rebooted then checked palette manager, everything ok. I've no idea where the log file for that npm update would be, sorry. If anyone can point me to it I'll happily include any info. NR and all nodes are now up to date thanks.
If it worked ok then don't need log I think. By log was meant the terminal output.
I wonder whether you ran it from the wrong directory, or forgot the unsafe-perms the first time.
Possible Colin - well, now theres a record here for future ref... been my lucky evening so far, updated NR nodes, then apt-update - apt dist upgrade, apt upgrade and apt autoremove.. all perfect. (all sudo of course). Then checked NR again, all fine, doing a clone.
over time - apt has become more in favour (though apt-get hasn't been deprecated) - so sudo apt update && sudo apt -yq dist-upgrade && sudo apt -yq autoremove && sudo apt -yq clean does it for me.
I think the 'official' command is apt full-upgrade rather than dist-upgrade though I see that dist-upgrade also works. I tend not to recommend apt for Raspbian yet as I don't think it works on Wheezy, but perhaps there are so few of those left around now though that I should not worry.
Personally I wouldn't use the -yq on the upgrade either, I like to see what it is doing just in case something has gone wrong and it says it is, for example, going to uninstall a load of stuff it shouldn't. That is just a personal preference however, probably more to do with my geek level than anything else.