Andrew, yes: I have been using Alfred from many many years now and that alfred.alfredpreferences file have been with me all this time. When I installed alfred 3 on my work laptop (almost 2 years ago), i just downloaded the file from my personal dropbox to ~/Documents and used it with no problem... Meaning: the lowercase `a` in there was never an issue before... The problem I'm highlighted here on this thread only started happening very recently, after upgrading to Alfred 4. Maybe the logic now clearly expects a case-sensitive path for the preferences file?
As for the commands to run... They never failed. I.e.: after running them they only returned the usual blank line back to the command prompot. I don't if I mislooked the first time (i think was only paying attention to the drwx* flags, not the @ symbol), but the @ symbol is actually no there indeed. Please note I have also made the file with a upperCase A now:
ls -lha
total 712
drwx------@ 5 myUser myGroup 160B Jul 24 09:40 .
drwx------+ 10 myUser myGroup 320B Jul 23 16:49 ..
-rw-r--r--@ 1 myUser myGroup 6.0K Jul 24 09:40 .DS_Store
drwxr-xr-x 10 myUser myGroup 320B Sep 28 2017 Alfred.alfredpreferences
-rw-r--r-- 1 myUser myGroup 345K Jul 1 2017 Emoji.alfredsnippets
I will see how it behaves until the end of the day and report here if that fixed it.
Thanks again for the help so far