Ok, thanks for telling me what to type in to create the file, that is helpful. The file flags.txt file appears now.
The console tap that appeared in Joplin (as the instructions said it would) didn't do anything, it just stayed blank/empty.
I created a to do, set an alarm, synced, the sync worked as usual, but the alarm didn't go off on desktop and no change in the console inside of Joplin.
The instructions do say "add", my mistake.
Going back to those instructions:
Now repeat the action that was causing problem. The console might output warnings or errors - please add them to the GitHub issue. Also open log.txt in the config folder and if there is any error or warning, please also add them to the issue.
The console did nothing. In the log.txt file I wouldn't know what to look for but nothing says error or warning. The instructions then say to add them to the issue, I don't know which issue, nor how to add them, or if there is anything wrong with them.
So still stuck, but have learned a few things so thank you, it hasn't been or nothing. But I am determined to get this working as well as continue to learn.