This is a standard option for cleaning corrupt databases - you can lose the relationship diagrams but that is it.
I've been using a database that I copied and I just opened the relationship diagram and found that my previous relationships were gone, replaced by three tables:
MSysNavPaneGroupCategories
MSysNavPaneGroupToCategories
MSysNavPaneGroups
Where did these alien tables come from and how have my previous relationships been affected? What happens if I change the relationships for these tables?
Can I remove them from the Relationships window and just add the relationships for my tables?
But how can all my forms still be working if there were no relationships between my tables? Does it save the relationships somewhere else?