http://forums.sugarcrm.com/f3/how-remove-custom-relationship-37781/
When you create a new relationship through Admin -> Studio -> <Module Name> -> Relationships, Sugar create several files at custom folders:
Left Side Hand Relationship (module from which you created the relationship):
custom/Extension/modules/<ModuleName>/Ext/Vardefs/<relationship_name>.php
custom/Extension/modules/<ModuleName>/Ext/Layoutdefs/<relationship_name>.php
custom/Extension/modules/<ModuleName>/Ext/Language/<relationship_name>.php
Right Side Hand Relationship:
custom/Extension/modules/<ModuleName>/Ext/Vardefs/<relationship_name>.php
custom/Extension/modules/<ModuleName>/Ext/Language/<relationship_name>.php
Relationship itself:
custom/metadata/<relationship_name>Meta.php
Table Dictionary:
custom/Extension/application/Ext/TableDictionary/<relationship_name>.php
After removing all these files you should need to go to Admin -> Repair -> Quick Repair and Rebuild
Cheers
Share
André Lopes