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You can define on what places WS looks for indexing, but this maybe make in the end no sense because of finding documents in general within windows.
Having the opportunity to switch it on and of gives you the freedom to have both: a little bit more speed when you need it and after you finish your work starting the service again and let Windows search update the index in the background.
You can make two batch files to switch it on and of or you can start calibre via one batch script (stop WS -> start calibre and doing your work -> stop calibre -> start WS) if you have bigger jobs to do with the libraries. That's maybe a better way
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