You can select specific file system shares and folders and apply different archive settings to them in the same archive job.
See About archive settings in the Archiving Option.
To apply different archive settings to file system share and folder selections for archive jobs
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In the task pane, under Archive Tasks, click New archive job.
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In the task pane, under Source, click File System Selections.
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Click Different archive settings to specific shares and folders.
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Click the share selection or folder selection for which you want to assign archive settings, and then click Assign Settings.
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Complete the options as appropriate.
See Archive settings options .
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Click each share selection or folder selection, and then click Assign Settings and create the archive settings that you want to apply.
See Creating an Archiving Option archive job by setting job properties.