AddMetaData filters out genes not shared between 2 objects

[rmenafra]

I have two different cellranger outputs of the same dataset, the newest one was run with a modified custom reference, the older has been fully annotated in Seurat (clustering etc). When I import both of them in seurat and try to transfer the metadata field of the clustering from the old object to the new one I cannot see anymore my "added genes". Basically I would like to see the expression level of the "added genes" without having to recluster the data. Is it expected that AddMetaData will drop the genes not common between the two seurat objects? If I don't try to add the metadata field I can see the expression of the added genes in the newes seurat object, so I am sure they are there.
I transfer the metadata as follows:

metadata_column <- "cluster_annotation"
new_libb$cluster_annotation <- old_libb@meta.data[Cells(new_libb), metadata_column]

Thanks
Roberta