QB Issue Resolution:

It’s possible that the payment was unlinked.

Let’s verify this by going to each invoices and apply all available credits. This way, it will be recorded as paid. Let me guide you with these steps:

  1. Click the + New button, and then select Receive Payment.
  2. Select a customer.
  3. Tick the open invoice under Outstanding Transactions.
  4. Click Save and new.

Repeat the same steps for the other unpaid invoices.

Also, for the journal entries, I’d recommend reaching out to your accountant. They can you on what to do with those entries without messing your accountant.

On the other hand, here are the list on what data are not included when converting to QuickBooks Online: Limitations when you convert from QuickBooks Online to QuickBooks Desktop.

Resolution for Issue 'After switching over to quickbooks online from desktop, there are hundreds of old transactions showing up (payments, invoices & journal entries) dating back to 2010. Any ideas how to clear these out without messing up the accounts?' available: Yes (Solved).
Source: Intuit Community forum.

After switching over to quickbooks online from desktop, there are hundreds of old transactions showing up (payments, invoices & journal entries) dating back to 2010. Any ideas how to clear these out without messing up the accounts?: 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.

Support for Clear Old Transactions
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Error Recovery for Clear Old Transactions [Canada]
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