Some files in folder desktop aren't shown on the desktop

Did you also adjust the "t" in this command?

ln -s ~/.var/app/org.mozilla.thunderbird/.thunderbird ~/.thunderbird
                             ^

If not, you probably need to delete the previous link first, and then run this with the capitalization adjusted as needed:

rm -rf ~/.thunderbird
ln -s ~/.var/app/org.mozilla.Thunderbird/.thunderbird ~/.thunderbird