Sounds like you want to select the shares being disposed of on a “maximum loss basis”. That is, you want to sell the shares with the highest cost base first.
This is a common method and is permitted by the ATO. Just keep a record of which ones you have disposed of and when, so you can calculate your crystalised CGT at tax time, and so you know the cost base of the ones you keep.
I use ShareSight to keep track of this for me. I have it set up to calculate all sales on a max loss basis. I have to pay a subscription fee but its tax deductible.
As always, speak to your Accountant or the ATO if you are unsure.
