For safety, I would delete the `.nef` files in a separate step after using `rsync` to transfer both types of files. For example, like this:

 rsync --verbose --archive --prune-empty-dirs \
 --include='*.nef' \
 --include='*.jpg' \
 --include='*/' \
 --exclude='*' \
 "$source/" "$target"

 find "$source" -type f -name '*.nef' -delete

The `rsync` command here would only copy the `.nef` and `.jpg` files (it would skip any other file, and it would not create empty directories at `$target` due to `--prune-empty-dirs`), and then the `find` command would delete all `.nef` files.

I tend to never use `--remove-source-files` with `rsync`.