It's almost always better to use the auto-update option and add new members or member information to your existing list.
If you're deleting and uploading new lists with the same recipients on a regular basis, this tends to cause abuse complaints. When you delete a list, the entire list history is lost (including unsubscribes, abuse complaints and bounces). And people who already asked to be removed can be added back to your list. Because all lists in MailChimp are independent of each other and share no information, there is no overall account suppression list. Our automated review process can note frequent deletes and abuse complaints based on deletes and we unfortunately sometimes have to suspend the account.
Using multiple lists is better, for example, if you have multiple clients you're working for in the same account.