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Hi Ryan,
Apologies for the terribly late response, we're just doing a bit of catch-up now. No doubt you've solved your problem by now, but it would still be useful to answer your question for other users with the same problem.
Many of the National Starter Data Sets were created with an older version of LEAP, one that didn't treat percent shares as strictly as the newer versions of the software. We're continually working to update and upgrade the data sets to improve compatibility.
The branches in the starter data sets are based on a template, and we don't always have the necessary information to fill the template for each country. Often the fuel shares under the Non-Ferrous Metals, and others, sum to zero, when in fact they really should sum to 100%. If there is no activity in a particular branch under the Baseline scenario, then you can safely remove the branch. This is basically what you have already suggested.
Best of luck,
Taylor