Due to the way that Import ID fields are named in the Blackbaud Raiser's Edge, it can be a bit difficult to determine at a first glance which Import ID is needed for the Relationship Synchronisation.
Below, you can see the Output tab of a Constituent Query where we have exported three different Relationship Import ID fields (Spouse Import ID, Individual Relation Individual Import ID and the Individual Relation Import ID. The Spouse Import ID is the same as the Individual Relation Individual Import ID. The field that you actually need is the Individual Relation Import ID.
When you are working in a Relationship Query (as you will need to do for the Relationship Synchronisation). this field is found under Individuals and is labeled as "Import ID".
For more information regarding the differences between these fields or where they can be found in the Raiser's Edge, we will defer to the team at Blackbaud. This knowledgebase article from their website may be of help.