Note that this setting does not control where files are stored - only whether linked files within the specified folder are referenced by absolute or relative paths. If you add a linked file within the base directory, Zotero stores a relative path to that base directory rather than an absolute path. For example, if the folder with your linked files is at /Users/Sarah/Dropbox on your laptop and at C:\Users\Sarah\Dropbox on your work computer, set those paths as the base directory on each respective machine. You should set the base directory to the folder on each computer under which you store linked files. This setting allows you to access linked files on multiple computers even when they're stored in different locations on each computer.
If you store attached files in Zotero - the default - this setting does not affect you.
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