Figured it out! I did a Search in the root folder without any criterion and they all showed up and I was able to move them into the originally intended folder.

If it is helpful, I used the following steps in Outlook 2010:

1. Click on the Search box above the email list - this reveals the Search Menu tab
2. Click Advanced Find... under the Search Tools dropdown in the Options grouping
3. In the dialog box, click the Browse... button in the top right and select only the root folder and uncheck Search subfolders at the bottom
4. Click OK
5. Click the Find Now button and the emails should show up
6. Select the emails you want to move and right-click to select Move and choose the folder you want them moved to

Hope this helps!