QB Issue Resolution:

this is a known problem and this problem has existed for over 5 years

Intuit is aware of it and ignores it, <-- my perspective the export to desktop 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 as service items with no history https://qboe.custhelp.com/app/answers/detail/a_id/1447

Resolution for Issue 'I have exported QBO to desktop and significant data is missing (i.e. all deposits). Has anyone every had data NOT export completely?' available: Yes (Solved).
Source: Intuit Community forum.

I have exported QBO to desktop and significant data is missing (i.e. all deposits). Has anyone every had data NOT export completely?: this 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 issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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