For future reference i managed to clear it up by using a slightly modified version of Girish's search command. It seems like the length limit applies to path length not just the filename length
find . -type f -print|awk '{print length($0), $0}' | sort -n
Went into the web interface and deleted / renamed files longer than 156 bytes and finally cleared trashbin/versioned files
(wipes all deleted / old versions of files - careful):
sudo -u www-data php -f /app/code/occ versions:cleanup
sudo -u www-data php -f /app/code/occ trashbin:cleanup
@robi @girish agreed it would be awesome if there was an automated way to handle this in the future