cd ~/Downloads/"PDF FOLDERS" && \
find . -mindepth 2 -type f | while read -r file; do \
  base=$(basename "$file"); name="${base%.*}"; ext="${base##*.}"; \
  if [ "$name" = "$base" ]; then ext=""; else ext=".$ext"; fi; \
  dest="./$name$ext"; i=1; while [ -e "$dest" ]; do dest="./${name}_$i$ext"; i=$((i+1)); done; \
  mv "$file" "$dest"; \
done && \
find . -mindepth 1 -type d -empty -delete