QB Issue Resolution:

The Upper Level or Parent Account Register shows all transactions in the subaccounts, by default. You really did remove Them, for real. You would not LOOK at the transactions from the parent level register and use it only for Reconciling, when you are tracking an actual bank account as subaccounts. Nothing gets posted to the parent level, directly, in this case.

You would never link accounts like this if these are real, separate, bank accounts, in reality, at the bank. They should not have a common parent.

All of these companies need to be using the same FEIN, or they should be separate data files.

Resolution for Issue 'why do the transactions from sub companies go into the main companies register?' available: Yes (Solved).
Source: Intuit Community forum.

why do the transactions from sub companies go into the main companies register?: 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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