Ansys Employee

Possibly, if you're using Fluent Meshing. I've not tried this but don't see why it won't work: test on a simple model. 

Split the solids rather than subtract from the fluid zone. You'll have the fluid zone and all of the solids. Share Topology and go into Meshing. Mesh, and set the solid zones as "solid", fluid zone as "fluid". When you read into Fluent the surfaces between the zones will retain some of the solid label. In Fluent you can then delete the solid zones from your model leaving behind the fluid and labelled surfaces. 

I also suggest reviewing either the copy feature in boundary conditions or TUI journals to speed up setting all the bc's.