Try doing this :
mkdir ../new_dir
find . -type f -name '*.epub' -exec mv {} ../new_dir/ +\;
if all the files are named name.epub, then you need to increment a variable like this (using bash )
mkdir ../new_dir
find . -type f -name '*.epub' |
while read a; do
((c++))
base="${a##*/}"
mv "$a" "../new_dir/${a%base%.epub}_$(printf %.03d $c).epub"
done