I just encountered this myself.  I had never noticed Payment Instructions in the Sales setup before, so I tried it out.  Realized it just prints in the same place as "message on invoice" which is not useful to me so I went back into company setup and deleted the custom payment instructions.  This did NOT change my existing invoice - they still showed the custom text, no matter what you type in the Message on Invoice in your invoice screen - but I was able to confirm that all NEW invoices no longer show the custom instructions.

Just another new QBO "feature" with no explanation as to how it actually works or what it does, that killed 30 minutes of productivity at the end of a long day and turned out to be useless. Thanks, Intuit!