I want to run a tblastn of a single protein sequence against a large number of genomes with each as a separate database so that each one generates a new file even if there is no match. This is important as I'm equally interested in genomes with it as I am for genomes without it. If there is a way to make one database create files for each genome this would work. The main point is just that I need a result file for each genome. The amount of genomes will be in the thousands so doing it by hand would be rather tedious. The genomes I have downloaded from from the ncbi database and have converted to individual databases with a script. If the individual file for genome isn't a feature of BLAST I will just write a script to BLAST the genomes one after the other.
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You will have to do that yourself, especially since you want an empty file if there is no match. You scripted creating the databases already so this task should follow along the same lines.