Yes, that should work. The top level script (make -C deps compile-llvm) simply checks for the existence of the libLLVMJIT library within the build folder. You could remove that to force it to execute LLVM makefile (which should do a minimal rebuild). But just running make within the LLVM directory should work, too. Note, though, that depending upon your system the top level script will run LLVM's Makefile with some additional flags.