QB Issue Resolution:

Don’t use the customer message field for one-off notes like that. There are limits to the number you can enter.

Instead, just type the note in a “description” column of a line in the detail section that is otherwise empty. No quantity, rate, item or amount. Then you have a “comment” line in the order.

Resolution for Issue 'How do I include a note that is different with each invoice?' available: Yes (Solved).
Source: Intuit Community forum.

How do I include a note that is different with each invoice?: 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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