The requirements for a payor to report an amount in box 48 of a T4A are that you must report amounts that you "pay" for fees of other amounts for services. Therefore, a payor is not allowed to report amounts in box 48 on an "accrual" basis.
From an accounting perspective and to avoid CRA conflicts in the reporting of the box 48 amount transferred to a business statement, the solution is to make an "accrual adjustment" entry in either the income side of the business statement or the expense side of the business statement based on whether the accrual adjustment required is a net positive or a negative amount.
As an example, if the box 48 amount covered payments that were accruals from Nov 2016 to Oct 2017, and the Nov 2016 and Dec 2016 invoices (paid in 2017) amounted to $2,000.00 but the accruals from Nov 2017 to Dec 2017 were $3,000, then an entry on the income side of the business statement would be made to add $1,000.00 to the income reported ($3,000 to be reported in 2017 less $2,000 already reported in 2016.
However, if in the above example, if the accruals from the Nov 2016 and Dec 2016 invoices (paid in 2017) amounted to $3,000.00 but the accruals from Nov 2017 to Dec 2017 were $2,000, then an entry on the expense side of the business statement would be made to add $1,000.00 to the expenses reported ($2,000 to be reported in 2017 less $3,000 already reported in 2016.
Either entry on the business statement (T2125) would be entered as "accrual adjustment" and could be easily supported if audited. This would avoid any conflicts with changing the amounts shown in box 48 of the T4A and also not require asking the issuer of the T4A to make an amendment to the T4A that technically he is not allowed to make.
