Merging / Concatentating BLAST Databases
There's an app for that, apparently. 


  Often we need to search multiple databases together or wish to search a specific subset of sequences within an existing database. At the BLAST search level, we can provide multiple database names to the “-db” parameter, or to provide a GI file specifying the desired subset to the “-gilist” parameter. However for these types of searches, a more convenient way to conduct them is by creating virtual BLAST databases for these. Note: When combining BLAST databases, all the databases must be of the same molecule type. The following examples assume that the two databases as well as the GI file are in the current working directory.
  
  Aggregate existing BLAST databases
  
  To combine the two nematode nucleotide databases, named “nematode_mrna” and “nematode_genomic", we use the following command line:

$ blastdb_aliastool -dblist "nematode_mrna nematode_genomic" -dbtype nucl \
  -out nematode_all -title "Nematode RefSeq mRNA + Genomic



So, you can use the blastdb_aliastool to create merged databases just like you asked for.