There is not a way to merge the two files. When you export your information from QuickBooks Online it will create a new file in the desktop edition. You will need to manually combine the information from the two separate files.
Resolution for 'Consolidating issue: 'Consolidating Online with Desktop version.' available: Yes.
The Consolidating issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the Consolidating issue yourself by looking for a resolution described in the article. If it is a complex Consolidating issue or you are unable to solve the issue, you may contact us by clicking here or by using other Consolidating support options.
For more information about resolving issues related to Consolidating in Quickbooks/QBO or to get support for the issue 'Consolidating Online with Desktop version.', click the link below: