adding and removing proteomes - all-vs-all blast

[ArtemPankin]

Hello. When adding and removing proteomes in the same run, it occurred to me that Orthofinder performs blast/diamond of all the original proteomes vs the added ones disregarding the fact that some original proteomes are commented out in SpeciesID. Apparently, removal of the proteomes happens at the later steps since the final output is as expected.

Is there a way to skip blasting the to-be-removed proteomes from the beginning, which seems unnecessarily time-consuming if many proteomes are getting removed from a previous run with a large data set? Thank you.