I am in the process of updating some annotations using the Ensembl Biomart.

Using the biomaRt package in R I do the following:

    mart = useMart("ensembl", dataset="rnorvegicus_gene_ensembl")
    transcript_mart = getBM(
    attributes = c(
        "ensembl_transcript_id",
        "ensembl_gene_id"),
    filters="ensembl_gene_id",
    values="ENSRNOG00000047860",
    mart=mart)

The result is empty. I check on the website and get a result:

    Ensembl Gene ID    Ensembl Transcript ID
    ENSRNOG00000047860    ENSRNOT00000073930

So the thing is: The website uses Ensembl Genes 71 (the example gene was added with the new rat genome assembly in 70).
I check the biomaRt package and it is the current 2.16.0.

    listMarts()
    biomart                      version
    1 ensembl ENSEMBL GENES 69 (SANGER UK)

tells me though that biomaRt 69 is current.

    listDatasets(mart)
                        dataset                       description version
    12 rnorvegicus_gene_ensembl Rattus norvegicus genes (RGSC3.4) RGSC3.4

And uses the old genome assembly.

If I check the [Biomart registry](http://www.biomart.org/biomart/martservice?type=registry)

Still the old version 69 marts are listed.

So the question is: Am I missing something or is the biomaRt package/registry simply out of date?
Yes, everything that you state is correct and it seems that version 69 is still the Bioconductor/biomaRt default.

You can use release 71 as explained in this post from the BioC mailing list: [Useful information about Ensembl release 71 mart databases](http://grokbase.com/t/r/bioconductor/134bx70fe3/bioc-useful-information-about-ensembl-release-71-mart-databases).

    mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                    host = "www.ensembl.org",
                    path = "/biomart/martservice",
                    dataset = "rnorvegicus_gene_ensembl")
    
    transcript_mart <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id"), 
                             filters = "ensembl_gene_id", 
                             values = "ENSRNOG00000047860", mart = mart)
    
    transcript_mart
     #  ensembl_transcript_id    ensembl_gene_id
     # 1   ENSRNOT00000073930 ENSRNOG00000047860