こんな感じのこと？

;; 文字コードてきとー
(defun hoge-func ()
(let ((in (read-file-name "入力ファイル: "))
(out (read-file-name "出力先ファイル: ")))
(with-temp-buffer
(insert-file-contents in)
(goto-char (point-min))
;; 正規表現てきとー
(while (re-search-forward "(@import \"\\([^\"]+\\)\")" nil t)
(let* ((fn (match-string 1))
(contents (save-match-data
(with-temp-buffer
(insert-file-contents fn)
(buffer-string)))))
(replace-match contents nil nil nil 0)))
(write-region (point-min) (point-max) out))))