Generally its all about replacing the files (old files are deleted, new files are unpacked)
The difference is:
Update throught the wordpress would / maight (depends if plugin is active or not, and if You run it from wp-admin/update-core.php or wp-admin/plugins.php site, and if it is bulk update or single)
- turn on/off maintenance mode
- create a lock file (to prevent parallel updates)
- silent deactivate / activate plugin
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