Making changes to the protein accession mapping file

I am using MEGAN CE v6.11.1 with to assign taxonomy to my contigs. I am having issues with taxonomic assignment of the most abundant species in my metagenome samples (Halohasta litchfieldiae), which might be due to the fact that NCBI has assigned different taxon-IDs to the complete and draft genomes of this organism. Since my lab has sequenced and submitted both versions, I know them to be a single species. The complete genome goes by the name halophilic archaeon True-ADL (Taxon ID 758602) and has 3,392 proteins, whereas the draft genome is called Halohasta litchfieldiae (Taxon ID 1073996) and has 6,628 proteins. We will be requesting this change from NCBI so that the future mapping files will automatically pick it up, but that might take some time. Is there any way to change the taxon IDs of the 3,392 True-ADL proteins from 758602 to 1073996 for now?