Home directory in terminal doesn't know about existing or newly created files and folders after Ubuntu upgrade

Question

After upgrading from Ubuntu 16.04 to 18.04.2 LTS I find only handful of my home directory contents when using the terminal (natutils sees them fine). Basically only Videos/ and a few files . However the files and folders are all still there. Autocomplete does not work if I start typing Documents/, but if I do ls Documents/ the content is all there.

Have been able to work around this since I know most of my $HOME/* folders and important files off by heart. Wanting to use du or rsync for the content in my home folder is basically impossible.

guillermo@guillermo-TECRA-A40-C:~$ du -hs $HOME/*
12K /home/guillermo/dungeon.txt
24K /home/guillermo/gerrit.ods
84K /home/guillermo/noise_nuisance_log.docx
44K /home/guillermo/print.pdf
659M    /home/guillermo/pyenv3
24K /home/guillermo/ranking_Cg_rank_0001_to_00-1.pdf
28K /home/guillermo/scripts
256K    /home/guillermo/v6_BSM_Coupling.tar.gz
22G /home/guillermo/Videos

which is not showing the content of Documents or tons of other folders and files:

guillermo@guillermo-TECRA-A40-C:~$ du -hs $HOME/Documents
6.1G    /home/guillermo/Documents

To further illustrate the severity:

guillermo@guillermo-TECRA-A40-C:~$ mkdir $HOME/folderexists
guillermo@guillermo-TECRA-A40-C:~$ ll $HOME | grep folderexists
guillermo@guillermo-TECRA-A40-C:~$ sudo ls $HOME | grep folderexists
guillermo@guillermo-TECRA-A40-C:~$ cd $HOME/folderexists
guillermo@guillermo-TECRA-A40-C:~/folderexists$ pwd
/home/guillermo/folderexists

folder permissions are fine:

guillermo@guillermo-TECRA-A40-C:~/folderexists$ ll .
total 52
drwxr-xr-x   2 guillermo guillermo  4096 Apr 16 10:51 ./
drwx------ 113 guillermo guillermo 45056 Apr 16 10:51 ../

I should also note that the $HOME directory is encrypted so I wonder if there is wonkyness going on in the mount.

---

requested output:

guillermo@guillermo-TECRA-A40-C:~$ type ll
ll is aliased to `ls -alF'
guillermo@guillermo-TECRA-A40-C:~$ type ls
ls is aliased to `ls --color=auto'
guillermo@guillermo-TECRA-A40-C:~$ /bin/ls -lah
total 752K
drwx------ 113 guillermo guillermo  44K Apr 16 10:51 .
drwxr-xr-x   5 root      root      4.0K Aug 16  2019 ..
drwx------   5 guillermo guillermo 4.0K May 16  2019 .adobe
-rw-r--r--   1 guillermo guillermo 1.6K Aug  6  2019 .davmail.properties
-rw-r--r--   1 guillermo guillermo 3.6K Jul 28  2019 dungeon.txt
drwxrwxr-x   2 guillermo guillermo 4.0K Jul 14  2019 .FBReader
-rw-rw-r--   1 guillermo guillermo  13K Mar  9  2017 gerrit.ods
-rw-rw-r--   1 guillermo guillermo  113 Apr  5  2017 .gitconfig
-rw-------   1 guillermo guillermo  72K Apr 14 09:13 .ICEauthority
drwx------   3 guillermo guillermo 4.0K Dec  7  2016 .kde
drwx------   3 guillermo guillermo 4.0K Jan 16 11:39 .launchpadlib
drwxrwxr-x   3 guillermo guillermo 4.0K Jan 25  2018 .matlab
lrwxrwxrwx   1 guillermo guillermo   34 Feb 26 12:45 .mbsyncrc -> /home/guillermo/.emacs.d/.mbsyncrc
-rw-rw-r--   1 guillermo guillermo  74K Oct  8  2018 noise_nuisance_log.docx
-rw-rw-r--   1 guillermo guillermo  33K Aug  1  2017 print.pdf
drwxr-xr-x   8 guillermo guillermo 4.0K Feb 19 09:05 pyenv3
-rw-rw-r--   1 guillermo guillermo  16K Feb 22  2019 ranking_Cg_rank_0001_to_00-1.pdf
drwxrwxr-x   2 guillermo guillermo 4.0K Jun  4  2019 scripts
-rw-r--r--   1 guillermo guillermo    0 Dec  5  2016 .sudo_as_admin_successful
-rw-rw-r--   1 guillermo guillermo 246K Jun 22  2018 v6_BSM_Coupling.tar.gz
drwxr-xr-x   4 guillermo guillermo 104K Feb  5 23:10 Videos

and with tree

tree -L 1
.
├── dungeon.txt
├── gerrit.ods
├── noise_nuisance_log.docx
├── print.pdf
├── pyenv3
├── ranking_Cg_rank_0001_to_00-1.pdf
├── scripts
├── v6_BSM_Coupling.tar.gz
└── Videos