Just what I was thinking, Paddy... thank you for confirming that for me! I have to admit I'm finding these new OS's so much more complicated and they make no sense compared to older OS X versions.
IMO, these OSs are in a way, tripping over themselves... there are things like .plists for example in 2 or 3 places when it seems to me, one was sufficient, like in the ~/Library and /Library folders. There are aliases in places like Library/Containers that seem to be the ones that break... the corresponding original in the place it should be isn't there. For why?
I'd like to know. Another place I find "stuff" is in the Preferences/By Host directories... that seems to another good place for broken aliases. And then... this one blows me away... in .private/var/folders etc. They are hard to find unless you have something in particular to look for as they are spread all over and looking through every folder and sub folder on the machine is a task I wouldn't assign even to a worst enemy!
I need to keep clearing old apps etc... I have a whole folder of stuff in my Downloads folder that are just stored items, many very old back to Classic OS's. High time to clean up here... what I really need is to learn how to search more efficiently with EasyFind where I'm not familiar with wildcards etc. and Terminal. I'm sure Terminal could turn up all the aliases in certain places so you could just go check them bit by bit. However my grasp of Terminal is pathetic... if I find a site that is reputable and has the commands in highlighted grey boxes then it is easy. I am NOT afraid of Terminal... just of entering the wrong syntax. So until I learn more myself or find the commands "handed" to me...
In one way however, the silver lining to the cloud... this expedition is proving to be good for waking up forgotten tech skills...
I like that...
The good news is that none of the busted aliases I've found so far seem to have affected anything. I found one broken one re: the saved state of my Notes.app however when I open Notes it is exactly where and the way I left it. *scratch my head** and move on... I did look around online re: the alias problem and again... I find many examples of weird things happening with aliases... broken, and other issues that seem to have started happening more with Mavericks and especially Yosemite, I never ran either however El Capitan has issues with them too. Perhaps when Apple started sticking things everywhere and all over.
One other horrible place is in both Libraries>Containers. Awful.
And on we go...
Oh... one hint for searching out broken aliases. In ~Library/Containers... just quickly look in each one in the Data folder in Documents and Library... that is where the most are in my case anyway... worth a check. I can quickly enough get rid of many of the issue aliases. In the Library folder once you've deleted them it seems to clear all of them, in the Documents folder I have a dead iChats alias in nearly everyone I've checked.