QB Issue Resolution:

For 2 companies you need 2 companies in QBO. I would leave everything in place up through 2016 and start fresh for 2017 with an additional file for the smaller of the two companies. Make sure your beginning balanes for 2017 are accurate per bank statements. If you reconciled correctly even though comingle expenses the bank accounts and credit card statements should have balanced on 12/31/16. If they don’t it means you over reported or underreported income or expenses for one or both companies. You can file amended returns, which is correct procedure, or you can leave the returns alone and post any adjustments in 2017 for what was out of balance (incorrect and potentially harmful if it changes reportable income significantly as in enough to make a difference in taxes)

Resolution for Issue 'Should I start over in Quickbooks Online after 3 years?' available: Yes (Solved).
Source: Intuit Community forum.

Should I start over in Quickbooks Online after 3 years?: 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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