There's something weird going on. Or miss configuration in my part. I just rebuilt my whole setup from scratch moved it to another host, etc.
This is the structure right now (looking at in from the host):
$ pwd
# note the directory we are in which is the same as the config directory
# Is the same directory I get when I ssh into the ssh addon or the hass_cli
/usr/share/hassio/homeassistant
$ ls -l
total 12928
-rw-r--r-- 1 root root 1171 Apr 26 03:06 automations.yaml
-rw-r--r-- 1 root root 3208 Apr 26 00:13 cloud.yaml
-rw-r--r-- 1 root root 8956 Apr 26 02:00 configuration.yaml
drwxr-xr-x 2 root root 4096 Apr 25 22:22 deps
-rw-r--r-- 1 root root 0 Apr 25 22:22 groups.yaml
-rw-r--r-- 1 root root 479913 Apr 26 03:32 home-assistant.log
-rw-r--r-- 1 root root 12627968 Apr 26 03:32 home-assistant_v2.db
# Here is all the flow data stored
drwxr-xr-x 4 root root 4096 Apr 26 03:00 node-red
# ---------------------------------------------------
-rw-r--r-- 1 root root 0 Apr 25 22:22 scenes.yaml
-rw-r--r-- 1 root root 0 Apr 25 22:22 scripts.yaml
-rw-r--r-- 1 root root 503 Apr 26 00:12 secrets.yaml
drwxr-xr-x 2 root root 4096 Apr 26 01:08 tts
-rw-r--r-- 1 root root 102 Apr 26 01:07 webostv.conf
-rw-r--r-- 1 root root 77824 Apr 26 03:25 zigbee.db
While all the other addons which get properly backed up have it's data in:
$ pwd
# Note where we are in the host
/usr/share/hassio/addons/data
ha@homeassistant:/usr/share/hassio/addons/data$ ls -l
total 32
# Every addon I have installed has it's configuration right here
# And all of them get backed up properly, I create a full snapshot download
# decompress and I get all their configuration and data but not with nodeRED
drwxr-xr-x 2 root root 4096 Apr 26 00:14 a0d7b954_nodered
drwxr-xr-x 3 root root 4096 Apr 26 00:21 a0d7b954_sonweb
drwxr-xr-x 2 root root 4096 Apr 26 00:14 a0d7b954_sqlite-web
drwxr-xr-x 3 root root 4096 Apr 25 23:56 a0d7b954_ssh
drwxr-xr-x 3 root root 4096 Apr 26 00:15 core_almond
drwxr-xr-x 2 root root 4096 Apr 25 23:53 core_check_config
drwxr-xr-x 2 root root 4096 Apr 26 00:14 core_configurator
drwxr-xr-x 2 root root 4096 Apr 26 03:27 core_mosquitto
# Here I list the nodeRED folder and that's all there is
$ ls -l a0d7b954_nodered/
$ -rw-r--r-- 1 root root 409 Apr 26 03:24 options.json
# options.json and when I do a full snapshot that's the only thing
# that's backed up from node red, none of my flows are backed up.
# All the data that has my flows is in
$ pwd
/usr/share/hassio/homeassistant/node-red
$ ls -la
total 156
drwxr-xr-x 4 root root 4096 Apr 26 03:00 .
drwxr-xr-x 7 root root 4096 Apr 26 03:43 ..
-rw-r--r-- 1 root root 35479 Apr 26 01:01 .config.json
-rw-r--r-- 1 root root 35231 Apr 26 01:00 .config.json.backup
-rw-r--r-- 1 root root 720 Apr 26 02:59 flows_cred.json
-rw-r--r-- 1 root root 668 Apr 26 02:59 .flows_cred.json.backup
-rw-r--r-- 1 root root 17245 Apr 26 03:24 flows.json
-rw-r--r-- 1 root root 17247 Apr 26 02:59 .flows.json.backup
drwxr-xr-x 3 root root 4096 Apr 26 01:00 lib
-rw-r--r-- 1 root root 2 Apr 26 02:57 node-red-contrib-home-assistant-websocket.json
drwxr-xr-x 2 root root 4096 Apr 26 01:00 nodes
-rw-r--r-- 1 root root 145 Apr 26 01:01 package.json
-rw-r--r-- 1 root root 85 Apr 26 01:01 package-lock.json
-rw-r--r-- 1 root root 7694 Apr 26 01:00 settings.js
I don't know the proccess homeassistant does when backing up, but doesn't seem to me like it's picking up node-red folder in the middle of my config directory.
If I'm not clear, or you have any doubts let me know, I tried my best. As I said this is a new install, new host, new VM, no restoring from previous snapshot, just setting up from zero. And this is the behavior I'm getting