It has been found that compressing your dgn file with Unused Item Type Libraries checked on will remove item type libraries from the file even if the item type is actually in use. This is because the software is not checking the sub elements in a cell to see if an item type is attached. OHDOT's sheet cells attaches an item type to the first sub-element in the cell.
Defect 692915 has been filed with Bentley Systems. Until this bug is fixed within the software it is recommended to leave Unused Item Type Libraries unchecked when compressing files.
The below video will go over the problem, how to fix the problem, and how to prevent the problem from happening in the future.