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Will killing the process cause problems if I shutdown and reboot immediately after doing it? I am running OS 11.2.3 (Big Sur) on Mac Mini.

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No. It just runs find command in the background to collect all file names and then it creates file name database from it. In any case you can simply rebuild the database by running

sudo rm -r /var/db/locate.database

and then

sudo /usr/libexec/locate.updatedb

in order to use locate command.

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