When you commenced a pension, it should be based on the market value of the assets supporting the pension at the date of commencement.
It would be a good practice to label the asset accounts clearly in your accounting software: segregated or non-segregated assets.
Put procedures in place so that cash inflows and outflows e.g (tax payable) come into and go out of the correct pension and accumulation bank accounts, the market value of the segregated assets will be equal to the member pension account balances at 30th June every year and at commence of the pension. Any tax refund will need to be banked into the correct pension and accumulation account.
If you commence a pension with segregated assets part way through the year, check that the income from the segregated asset in the taxation return is only exempt from the time the pension commences.
Once your accounting software is set up correctly, any capital gain or loss on the sale of a segregated asset will be disregarded.
Ensure that the fund will not have any cash flow issues regarding the payment of the minimum pension amount. Where this issue may occur is if you only have one property and a small bank account balance as the segregated assets,
The investment strategy may have to be updated due to the use of the segregation of the assets.
It would be a good practice to have a minute every year that lists the segregated assets and their market value.