Recently while inserting a custom entity (Transaction) records using the CRM Destination Component we realized that Contact’s lookup was not being set.
We were using Alternate Key to set the lookup as shown below
To get it working we had to uncheck the Remove Unresolvable References option from the Optional Settings of CRM Destination Component. It seemed that it ignored it, even though values were there for the GCR (alternate key field) in the input source.
I think it might not be working as expected in case if lookup is done using Alternate Key.
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Give it a try à
Hope it helps..