The easy part first:
Reports can only draw upon transactions during the defined period between From and Until dates. Think about the sources of information. The VAT Calculation Worksheet does not “know” what payments you have made to the tax authority. It basically only “knows” about taxes assessed and paid on sales and purchase transactions during the defined time frame. (Technically, it also knows about taxes assessed or paid on debit and credit notes, journal entries, and so forth. My point is that it tracks transactions affecting Tax payable.)
The worksheet is only meant to calculate figures related to the defined period. It is not a tax filing form to determine what you owe the authority. It’s figures do not take into account whether you have over- or underpaid at any time in the past.
So you are right. The worksheet is correct for what it is designed to do. If you overpaid in the past, that seems to call for an amended filing or adjustment to the current filing, but not a change to worksheet calculations for the current period.
Now for the more complex part of your inquiry:
It still is not clear exactly what happened. In your first post, you say your accountant entered the 92.72 as a journal entry in April. In your second post you describe a credit and debit to Business Mileage in March. Did your accountant make an entry in your Manager records? Or in her copy of your records? In other words, just how did she make this entry and where? What accounts did she debit and credit for how much? And why did you also make an entry? (Or are you just saying she instructed you in April to make an entry and you did so with the journal entry dated in March?)
Then we have the fact that journal entries are always tax-inclusive when a tax code is applied. A 20% VAT amount of 92.72 corresponds to an underlying transaction amount of 463.60. If you were making journal entries with such a transaction amount, the tax-inclusive figure you should be using is 556.32. So I do not see where you got your 548.88 number.
It also isn’t clear how the 1.24 difference enters the picture. Is that included in the 92.72? Subtracted from 92.72? Please explain further.
Overall, it seems you are trying to rectify a prior failure to apply a tax code to mileage expenses by crediting the expenses without a tax code and debiting them back with a tax code. Do I understand correctly?
If so, I wonder why you don’t just correct the original expense entries. I also wonder how you are calculating the expenses. It sounds like you are probably using a standard rate. If so, is that possibly already inclusive of VAT considerations? If it is, it is not appropriate to further burden the expense with VAT. If it is not, and the original expenses must have VAT added, a journal entry doesn’t strike me as the best way to accomplish this. Instead, I would use a supplemental expense claim. A journal entry is problematic because it needs to balance debits versus credits. And what you seem to be attempting is to balance an untaxed expense against a taxed expense. There is an inherent mismatch you cannot resolve as you described. (Or at least as I think you described.)