What are the recommended strategies and packages to reduce RNAseq data from ENSEMBL gene IDs to protein coding genes with a valid NCBI.ID? I normally use the package annotables and then filter for “protein_coding” and !is.na(entrez). After that I come up with a few duplicated entrez IDs, what’s the best way to deal with those?

This support site is intended to provide technical help for people using Bioconductor packages. The annotables package isn't a Bioconductor package, and you don't have a technical question, per se. You might try at biostars.org.