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You can apply transformation without break link.

Dim asm As AssemblyDocument = ThisDoc.Document

Dim boxOccurrence As ComponentOccurrence = asm.ComponentDefinition.Occurrences(1).Definition.Occurrences(1)

Dim mtx As Matrix = boxOccurrence.Transformation
mtx.Cell(1, 4) += 1

boxOccurrence.Transformation = mtx