Assume it is a 3 month contract(2/1/2020 to 4/30/2020) and billing day of the month is 1.

Note: I have chosen unit price of the product as 29$ because February has 29 days(to simplify the proration). 

--Initial Order--

Product A   1(Ordered Qty) - 29$(unit price) - 02/01/2020(Start Date)- 04/30/2020(End Date)

Customer is Invoiced on 02/01 for a total amount of 29$ and details are as below:

Let's say this is Invoice-1

Product A   29$(29$ unit price * 1 qty) for the period 02/01/2020 to 02/09/2020

--Amendment Order--

On 02/13/2020 customer doubled his order and the amendment order is as follows:

Product A   1(Ordered Qty) - 29$(unit price)- 02/13/2020(Start Date)- 04/30/2020(End Date) 

Invoice scheduler ran on 02/13 and created two Invoices as follows(I don't understand why it created two invoices):

Let's say this is Invoice-2

Product A   58$(29$ unit price * 1 qty * 2 months) for the period 03/01/2020 to 04/30/2020

Let's say this is Invoice-3

Product A   -75$(29$ unit price * 1 qty) for the period 02/13/2020 to 04/30/2020

Product A   34$(29$ unit price charged for 17 days for quantity 2) for the period 02/13/2020 to 02/29/2020

Total of Invoice-1,2 and 3 comes to correct number, which is 46$ but my question is what is the need of Invoice-2 and Invoice-3, why couldn't it just create one Invoice as follows:

Product A   17$(29$ unit price charged for 17 days) for the period 02/13/2020 to 02/29/2020

Anyone seeing this kind of extra Invoices where it could be just combined into one Invoice? This is so confusing for our reps and customers.  

Please note I have already looked into Invoice grouping article.