A late fee automatically added by Syncro to invoices is treated as a non-inventory item and thus syncs over to QB using the Default QuickBooks Product defined in your QuickBooks settings (see https://yourdomain.syncromsp.com/quickbooks/settings or Admin > Apps > Quickbooks > Sync Settings).
If you want a specific late fee item to sync to QB, you will need to create your own Late Fee item in your Products & Services and then manually add it to any late invoices.
If the late fee is non-taxable, then make sure the Default QB Tax code for non-tax items is set to a non-taxable QB code (found on the same settings page).
You will also need to make sure none of your Payment Terms include a late fee so that you can manually add your own.