Hello,
Yes, Windows Task Scheduler is the best way to schedule an automated task. BC3 supports scripting on the command line. Your command line call would be bcomapre.exe @script.txt
You can find scripting reference in the Help file under the section Using Beyond Compare -> Automating with Scripting (and Scripting Reference). There are sample scripts available there as well.
Let us know if you have any questions.
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