Solved.
I thought the commands were written individually, but the arguments need to be written all on the same command line.
For anyone having the same problem:
Find the BuildPatchTool directory using the command “cd C:.…YOURDIRECTORY…\Engine\Binaries\Win64”
If you just type “BuildPatchTool.exe” the program will open and close with error 3. Instead, type “BuildPatchTool.exe -mode"UploadBuild” -ClientID=“YOURCLIENTID”" etc… The other necessary parameters are described in the documentation .