Hi Ben,
John, thanks for the comments, my answer below should give you a better idea of why you had to go through this process when you converted your own account.
Unfortunately there is no easy way to convert your Method account if you switch from Quickbooks Desktop (QBD) to Quickbooks Online (QBO). The issue here is because of how Quickbooks has it setup, we can only reference data from either QBO or QBD at one time. Method must access two separate Quickbooks API's; QBO uses "IPP" and QBD will access data through the Quickbooks SDK. With that said, because of the way we must access the data, even if a customer is able to convert their Quickbooks file from QBO to QBD using an Intuit tool, there is nothing setup from Quickbooks for a 3rd Party Application to recognize this conversion correctly. Each type of Quickbooks account creates a Unique ID for each record, so when a file gets converted from one type of account to the other, this Unique ID used as reference gets changed. This leads to third party applications to think that two records appearing the same to you, are actually completely different records.
-Method_Ben