This issue was resolved with a hotfix in Blackbaud Hosting Services run on 6/27 and 6/28/18. If you are encountering this issue in a locally-hosted Raiser's Edge database, contact support and reference this article.
In the meantime, the following may help avoid this issue:
- After deleting a row, click into the top row that shifted up after deleting.
- Press (or press and hold) Tab to move the cursor through the remaining cells of the row.
- Once the cursor has moved down to the next row, the batch can be saved as normal.