Try using this custom version of
/mnt/ext1/system/bin/koreader.app:
Code:
#!/bin/sh
openWith="/mnt/ext1/system/config/handlers.cfg"
if ! grep -q "$1" $openWith; then ebookDir=$(dirname "$1"); fi
if [ "$ebookDir" == "/mnt/ext1/Digital Editions" ]; then
echo "${1}:eink-reader.app" >> $openWith
exec /ebrmain/cramfs/bin/eink-reader.app "$1"
else exec /mnt/ext1/applications/koreader.app "$@"; fi