this isn't related to game files tho, it can't find the bootstrapper. Change it back to cd /D, leave that bottom line alone, just change stuff on top where the comments are.
Wondering if maybe the "&" in your windows username could be an issue.. maybe the path gets fucked by that somehow.
What you could try is installing the client into the bo2 folder instead of appdata, to do that first edit !updatePluto.bat and change it to this:
plutonium.exe -update-only -install-dir ./plutonium
then change the server startup batch file line 19 to this
cd ./plutonium
now first run !updatePluto.bat and then the startup file.
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