I believe you will discover the VAT number is a custom field, placed according to your localization. Does the VAT number appear anywhere on the View screen of the invoices? You really need to post screen shots of Edit and View screens for an affected invoice. Otherwise, we are guessing what you mean.
Creating a test business with test data is the best way of addressing this issue. Doing so also increases the probability a solution will be found as it helps identify the minimum requirements to reproduce the issue.
To debug start by using the standard theme.
If it is a problem with your custom theme you will need to take primary responsibility for debugging it.
ok let me remove the cloning issue then, and I will stick to the other issue which is far more problematic as all my records for the last 5 years have lost their details.