Hi Gumu,
both software are demo code and provided "AS IS".
The newer code base is the MM9Z1J638-Demo-APPSW.zip and probably the better starting point.
MM9Z1J638-Demo-APPSW.zip contains various projects and a documentation.
Is targeting the standard EVB (KIT9Z1J638EVM), the 12V reference designs with LIN or CAN interface RD91Z-638-12V-L / RD91Z-638-12V-C
RD9Z1-638-4LI_APPSP.zip is a specific demo targeting the 4-cell LiIon reference design (RD9Z1-638-4LI)
Rgds
W.