Good day, Susan!
For the example you sent (Thank you for the scan!), and others like it, I would suggest using square symbols of shape to represent the boxes representing omission.
This preserves the print's use of "boxes" and lets the reader know how many omissions are indicated.
Since this transcription is for a 4th-grader, the square symbols of shape should be appropriate to the student's knowledge of Nemeth.
If you have further questions or concerns, please do not hesitate to share them.