When you migrating data from QB Desktop, system will migrate the whole data to QB Online, You have to create a new company file with no transactions on your QB Desktop if required. Another option, you may have 2 ways:
1. Utilize a 3rd party tool to migrate only the CoA and Lists. i.e TPExporter for Desktop, TPImporter for Online
https://transactionpro.grsm.io/qbo
2. Purchase a 3rd party service.
