May be a jsfiddle may help a lot, The code snippet is missing a lot of information。And I’ve encounted similar issue with you, see Access instancedMesh's sub-instance origin and tranform with pivot Appreciate any help 
May be a jsfiddle may help a lot, The code snippet is missing a lot of information。And I’ve encounted similar issue with you, see Access instancedMesh's sub-instance origin and tranform with pivot Appreciate any help