You do not have to combine license files.
Each license file that has any counted lines (the number of licenses field is >0) requires a server. It is perfectly OK to have any number of separate license files, with different lmgrd server processes supporting each file. Moreover, since lmgrd is a lightweight process, for sites without system administrators, this is often the simplest (and therefore recommended) way to proceed. With v6+ lmgrd/lmdown/lmreread, you can stop/reread/restart a single vendor daemon (of any FLEXlm version). This makes combining licenses more attractive than previously. Also, if the application is v6+, using dir/*.lic for license file management behaves like combining licenses without physically combining them.