I will do this before the end of the month.
The UE uses the same mapping files, however it is bundled with the tools that are used to create the mapping file:
The program MEGAN6UE/tools/ncbi/make-acc2ncbi creates an initial mapping file from data downloaded from NCBI
The program MEGAN6UE/tools/utils/extend-mapping is then used to extend the mapping file by assuming that all accessions that appear on the same header line belong to the same taxon: they are all assigned to t the LCA of all taxa that can be identified for the line.
To run these programs you need to use a server with 100+GB.