*shrugs* Beyond me. I am kinda new to snaps. 
[EDIT: removed incorrect observation]
Are you using any container systems? Is systemd your init system?
I am using systemd yes. No real containerisation per se. Encrypted hard drive though and btrfs /home for snapshoting
Thatās all fine. Iām still wondering what has happened. I wonder if the system will be back to life if you reboot (though please check systemctl status before and after, some services may have failed with interesting information).
Already rebooted today 
I could purge the install and try again. Not sure if that will do anything and certainly wonāt explain what is going on right now.
Please hold on for a few more hours if you can. Your system may have some important details about what has happened.
Did you check system logs / journal for any clues? Do you have any cron jobs / backup scripts that may have messed up /snap by accident?
Nope. I only installed snapd a week or so ago just to see if it worked. First app I have installed is castersoundboard. Then the Warzone2100 and finally Krita just to test. Here is the log for snapd from the journal:
Edit:
Actually this is the whole log.
journalctl -xu snapd
-- Logs begin at Wed 2017-09-06 09:53:17 BST, end at Wed 2017-09-06 13:12:37 BST. --
Sep 06 09:53:17 kratoforn systemd[1]: Starting Snappy daemon...
-- Subject: Unit snapd.service has begun start-up
-- Defined-By: systemd
-- Support: https://www.debian.org/support
--
-- Unit snapd.service has begun starting up.
Sep 06 09:53:18 kratoforn snapd[1190]: 2017/09/06 09:53:18.180005 daemon.go:252: started snapd/2.27.4-1 (series 16; classic; devmode) debian/unknown (amd
Sep 06 09:53:18 kratoforn systemd[1]: Started Snappy daemon.
-- Subject: Unit snapd.service has finished start-up
-- Defined-By: systemd
-- Support: https://www.debian.org/support
--
-- Unit snapd.service has finished starting up.
--
-- The start-up result is done.
Sep 06 11:38:18 kratoforn snapd[1190]: 2017/09/06 11:38:18.508076 snapmgr.go:429: No snaps to auto-refresh foundOk something weird is going on here. You know I did snap refresh and there was nothing to refresh. I just did snap refresh core and it pulled a newer core down. However, something odd seems to have happened in that a new /root/snap dir has been made which has castersoundboard and core in it.
ls -l /root/snap
total 8
drwxr-xr-x 4 root root 4096 Sep 6 13:22 castersoundboard
drwxr-xr-x 4 root root 4096 Sep 6 13:25 core
Is that supposed to happen?
Oddly enough though, now when I run castersoundboard as a nornmal user it works. So aside from a new core nothing else seems to have changed.
snap list
Name Version Rev Developer Notes
castersoundboard 0+git.c41a4f2 34 rikai -
core 16-2.27.5 2774 canonical core
krita 3.2.0 26 krita -
warzone2100 3.2.3 5 diddledan -
Curiouser and curiouserā¦
Yes, this is harmless. This is $SNAP_USER_DATA for the root user.
I think it works because you now have a valid core snap.
PS: Use triple backtick for things like shell output, it has nicer non-proportional font and thus output looks more like a terminal.
Fairy nuff.
Well seems whatever happened it has fixed the other apps as well. So question remaining is why did snap refresh not auto update core? I would have thought that would have been a prerequisite no?
I think it didnāt update it because it failed at some earlier stage because it count not access the meta/snap.yaml file. Can you paste the log for snap changes please? If there are any errors there please also paste snap change XXX replacing XXX with the number of that change.
ID Status Spawn Ready Summary
22 Done 2017-09-05T16:30:51Z 2017-09-05T16:30:51Z Refresh all snaps: no updates
23 Error 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Refresh "castersoundboard" snap from "edge" channel
24 Done 2017-09-05T21:38:50Z 2017-09-05T21:42:34Z Refresh "castersoundboard" snap from "edge" channel
25 Done 2017-09-05T23:10:57Z 2017-09-05T23:14:40Z Install "warzone2100" snap from "beta" channel
26 Done 2017-09-05T23:29:22Z 2017-09-05T23:29:22Z Refresh all snaps: no updates
27 Done 2017-09-05T23:30:54Z 2017-09-05T23:33:56Z Install "krita" snap
28 Done 2017-09-05T23:36:48Z 2017-09-05T23:39:08Z Refresh "krita" snap from "beta" channel
29 Done 2017-09-05T23:40:13Z 2017-09-05T23:40:13Z Refresh all snaps: no updates
30 Done 2017-09-05T23:41:39Z 2017-09-05T23:41:40Z Refresh "krita" snap
31 Done 2017-09-06T09:25:06Z 2017-09-06T09:25:06Z Refresh all snaps: no updates
32 Done 2017-09-06T09:35:12Z 2017-09-06T09:35:12Z Refresh all snaps: no updates
33 Done 2017-09-06T12:23:48Z 2017-09-06T12:25:32Z Refresh "core" snap
34 Error 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Install "lonewolf" snap
Nope. Canāt see any errors there. But you can see I did refresh and then I did refresh core. So not sure why it was in such a odd state.
Edit: last error was me trying to install new app when I terminated to get the log. The other error was a interrupted download last night. Some reason it just froze even though the rest of the internet was working fine.
Can you show the error for changes 23 and 34 please? Just in case thereās something interesting there.
Like I just explained. 23 was a frozen download.
Status Spawn Ready Summary
Error 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Download snap "castersoundboard" (34) from channel "edge"
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Fetch and check assertions for snap "castersoundboard" (34)
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Mount snap "castersoundboard" (34)
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Stop snap "castersoundboard" services
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Remove aliases for snap "castersoundboard"
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Make current revision for snap "castersoundboard" unavailable
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Copy snap "castersoundboard" data
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Setup snap "castersoundboard" (34) security profiles
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Make snap "castersoundboard" (34) available to the system
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Set automatic aliases for snap "castersoundboard"
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Setup snap "castersoundboard" aliases
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Start snap "castersoundboard" (34) services
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Clean up "castersoundboard" (34) install
Hold 2017-09-05T21:35:55Z 2017-09-05T21:38:46Z Run configure hook of "castersoundboard" snap if present
......................................................................
Download snap "castersoundboard" (34) from channel "edge"
2017-09-05T22:38:46+01:00 ERROR unexpected EOF
and 34 was me interrupting it.
Status Spawn Ready Summary
Error 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Download snap "lonewolf" (32) from channel "stable"
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Fetch and check assertions for snap "lonewolf" (32)
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Mount snap "lonewolf" (32)
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Copy snap "lonewolf" data
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Setup snap "lonewolf" (32) security profiles
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Make snap "lonewolf" (32) available to the system
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Set automatic aliases for snap "lonewolf"
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Setup snap "lonewolf" aliases
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Run install hook of "lonewolf" snap if present
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Start snap "lonewolf" (32) services
Hold 2017-09-06T12:42:12Z 2017-09-06T12:42:39Z Run configure hook of "lonewolf" snap if present
......................................................................
Download snap "lonewolf" (32) from channel "stable"
2017-09-06T13:42:39+01:00 ERROR context canceled
I think this is fixed now. Please comment if you find any new issues.