Unfortunately, you do lose all activity data for those people once they are deleted.
I would first troubleshoot the list of people being deleted and make sure to pull out any others who may have completed an engagement activity worthy of not being deleted. If so, perhaps design smart campaigns that look for any engagement activity and remove them from the list of those to be deleted.
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Always backup any deletions. Never automate this. Always check the counts carefully and review the export list BEFORE deleting.