Explanation
One scenario that could prevent an administrator from changing the relationship between work item and project custom objects from master-detail to lookup is that roll-up summary fields exist on the master object (project). Roll-up summary fields are fields that calculate values from related records in a master-detail relationship; they cannot be used in a lookup relationship. If roll-up summary fields exist on the project object, they would prevent the administrator from changing the relationship type unless they are deleted first. A junction object is not required to support a lookup relationship; it is only used when creating many-to-many relationships between two objects using two master-detail relationships. The lookup field in all the records containing a value or the lookup field being required for saving records are not scenarios that would prevent changing the relationship type; they are scenarios that would allow changing the relationship type without losing data or functionality. References:
https://help.salesforce.com/s/articleView?id=sf.fields_about_roll_up_summary_fields.htm&type=5
https://help.salesforce.com/s/articleView?id=sf.relationships_considerations.htm&type=5