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Items can become orphaned when the course you are copying into has less sections than the course you are taking content from.
You will be able to see orphaned items when you have editing turned on but not when when editing is turned off, students cannot see orphaned content.
Follow the instructions below to resolve this issue:
1. Click Edit settings under Administration
2. Expand the Course format section and click the drop down next the Number of sections and select the number of sections total you would like to have.