This is a known problem, intuit posted this as a possible work around

https://community.intuit.com/articles/1145619-exporting-data-with-internet-explorer-11-errors-when-i…

As an FYI

the export to desktop (US Only) provides you with a file that must be opened in desktop within 10 days, and the file has known problems, some things do not export, inventory exports […]

Resolution for 'both company issue: 'Export from Quickbooks Online from Internet Explorer 11- I am not able to export from IE11 so I can import into QB Desktop. Are there any solutions?' available: Yes.

The both company 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 both company issue yourself by looking for a resolution described in the article. If it is a complex both company issue or you are unable to solve the issue, you may contact us by clicking here or by using other both company support options.

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