Finally I could run ndown.exe for my domain 3. I just needed wrfout_d02 and wrfinput_d03 files.
I renamed them as wrfout_d01 and wrfndi_d02 and followed what tutorial says.
ndown creates wrfbdy_d02 and wrfinput_d02 as expected.
I have to rename them to wrfbdy_d01 and wrfinput_d01 according to the wrf manual.
Actually, these 2 files refer to my domain 03. At this step, I already changed my namelist.input from 4 domains to 2 domains, moving all corresponding columns: domain 3 becomes domain 1 and domain 4 becomes domain 2. Then, DX and DY should match with the new wrfinput files.
I did it as well in the namelist.wps because I needed to rerun real.exe so I can get a new wrfinput for domain 2 (actually domain 4).
When I run wrf.exe, I got mismatch between dx,dy file and namelist. It happens when I use wrfinput file from ndown. I also tried with the old wrfinputs from my 4 domains run (wrfinput_d03 as wrfinput_d01 and wrfinput_d04 as wrfinput_d02), but I have the same error.
When I use wrfinput_d01 (actually domain 03) and wrfinput_d02 (actually domain 04) got from real.exe I ran after ndown, it seems to work.
Any idea about this new problem?