Found that changing the call to sqla.exe that SQL Assistane does close and the .bat file continue to run.
CD \Program Files (x86)\Teradata\Client\13.11\Teradata SQL Assistant\
start /MAX /WAIT sqla.exe -c ADM -f \Teradata\ExportQueries\wa\FNCM_Info.sql -e \Teradata\DataExport\wa\FNCM_Info.csv
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