In my MCP, I have two reobfs scripts:
mcp/reobfuscate.sh and mcp/reobfuscate_srg.sh (For windows, you'd use the .bat versions.) These two scripts just call python scripts anyway, so the .sh/.bat is mostly just cosmetic. Anyway, find out where those scripts are getting their class files and make sure yours are in the right place. (ie, you need to call recompile.sh first)
I always use mcp/reobfuscate_srg.sh when I compile my mods. I haven't used the mcp/reobfuscate.sh script.