Whenever a lead enters Marketo, it is being deleted automatically.
Marketo will never delete any lead records on its own unless you have setup a trigger or batch campaign to do so. We suggest you to review your campaigns in Campaign Inspector and check for the campaign that is using "Delete Person," or "Delete Person from SFDC" with the value true for "Delete in Marketo."
If you have figured out the campaign and you would like to restore the deleted leads, contact support (https://nation.marketo.com/docs/DOC-1670-about-support) and they may be able to restore the deleted leads with a buffer period 30 days from the date of lead deletion.
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