Can list and see files/dirs in Console, but missing dirs/files if listing via SFTP client

First off I’m a linux newb, trying to follow instructions found on the 'net. So bear with me if I’m missing the obvious.

I’m trying to troubleshoot a droplet that won’t load due to a kernel panic. Screenshot - https://gyazo.com/ef9bb5fe876076b414c0fb0de34a804b

So I can log on using recovery image, mount the disk image and chroot into the system.

Now if I cd into /boot/ I can see a list of images and other files/dir. If I do the same for the /var/ I can see the www directory listed

BUT if I log on using a SFTP client (SmartFTP & Winscp), using the provided temp root password, I can not see the same list in /boot/, nor can I see the /www dir in /var/.

Opening a terminal window from within those clients also fails to see these directories and/or files.

Screenshot of /boot/ in DO console -https://gyazo.com/4f77c5f1ab2b8f068f076ebf737fbd57

same dir but using sftp client https://gyazo.com/275949d69a7ee61b23c6ec89cd25820f

/var/ in console https://gyazo.com/a32a2ddd077cdf147a75ad7d7b26ce22

/var/ from sftp client

https://gyazo.com/f3600697102f4827cb6077b74232655c

So can someone point out what I’m doing wrong here and how to fix the issue of the missing dir/files in sftp. cheers Steve