After the initial sync has been initiated, the only options for adjusting the field mapping between Marketo and Salesforce is through Marketo Support.
Once the new field in Salesforce is created and shows up in Marketo, Marketo Support has two approaches that can be taken, either merge the new custom field with the pre-existing one or move the mapping from the new custom field onto the original field You'll want to populate the new custom field with the values your Leads already have from the original field.
This is allow the system to queue up and sync the values to Salesforce. If a field merge or remap is done without the values being prepped it can results in values in Marketo not being pushed up for records. For the difference between a field merge and remapping, it's really personal preference but we definitely prefer field merge. This is a cleaner approach as the two fields will be combined resulting in a single field with the Salesforce mapping.
If a remapping is performed you'll still be left with two fields, just the mapping has been moved so then the discarded field will remain and need to be hidden or re-purposed. Field merges can only be performed on two custom fields.
If one of the fields in question is a Marketo Standard Field then a remapping will have to be performed. I hope this helps to shed some light on the situation!