The “rules” did not change. The taxable transactions were always the sales invoices, not the receipts recording money received against them. What changed was that the program previously allowed you to apply tax incorrectly on a line item posted to Accounts receivable. This resulted in your invoices appearing to be paid in full, but it meant that the tax amount was being counted twice, once on the sales invoice and again on the receipt. So, if you relied on Manager for reporting output GST, you probably over-reported for all those sales. That means you have a bigger problem than the challenge of correcting thousands of past receipts (not invoices). You may need to correct past tax filings.
No, I did not say the tax code was ignored in previous versions. I just said it was ignored. But I could have been clearer. Your question about “why does the current version still have a ‘Amounts are tax inclusive’ checkbox” and your statement that “older versions handled the taxcode situation correctly” were in the same paragraph. I interpreted them (apparently incorrectly) as being about the same subject, the checkbox. You had not checked the box on any transactions you showed, so it really did not make any sense to me for you to be making the point at all. Since the comment did not seem important, I gave it only a brief answer. From my original understanding of your question, I should have said something like “the new version of the program would have ignored the checkbox if you checked it.” Based on what you have now written, I see that you thought I meant the program was ignoring the tax code itself when you erroneously applied it to receipts recording settlement of sales invoices. I apologize for not explaining in greater detail.
The program has always treated tax codes the same way as far as they affect this subject. The change is that it previously allowed you to apply them in situations where you should not. In other words, it assumed you knew when to apply a tax code and gave you the flexibility to make an accounting mistake—thousands of times. Now it won’t allow that.
All your sales invoices are fully compatible. Your receipts are what requiring correcting. Every line item on a receipt posted against Accounts receivable needs to have its tax code removed. And the unit prices need to be changed to match the full amount receivable on the corresponding sales invoices including the tax. This is best done, as @Patch said, using Batch Update. The tax codes are easily removed. Changing the unit prices will probably be easiest to change by adding some columns for extra calculations during the spreadsheet phase of the update, then removing the old unit prices.
As a forum moderator, I am the wrong person to ask. But I doubt the developer will incorporate code to correct users’ past accounting mistakes. You speak of this as a revised format. But it is not. The program no longer allows you to make the same mistake again. The program’s logic did not change.