Duplicate genes with RSEM counts: Which one to choose?
There is no one-to-one mapping of gene ids from one database to the other. Ensembl (who maintain Ensembl ENSG IDs), ncbi (who maintain EntrezGene IDs and RefSeq transcript ids) and HUGO (who maintain gene symbols/names) all have different ideas about what a gene is, which part of the genome belongs to which gene etc. 

In fact, it's worse than that because HUGO gene IDs refer to the abstract idea of a gene, rather than a particular part of any chromosome. 

My suggestion would be to leave the IDs as Ensembl IDs (as these actually refer to a physical part of a chromosome, which is what you are quantifying), right up until you have to report the results to someone who really NEEDS gene names. If you still have duplicates, you could sum, or pick the most interesting, but I would suggest just leaving the duplicates in there, and treat it as thought there are two genes with the same name.