I found a way to shrink my product packaging, should I change it with my next order?
Will it cause any system issues if Amazon sees two different packaging sizes if I still have the old size still in inventory? Will it cause any problems with my listing?
Not at all.
There will be no issue and amazon will keep changing according to the packaging size.
If size shrink and its fba fee needs to revise then you can contact with seller support to remeasure my package and charge fba fee according to size tier.
It may or may not matter if you are downsizing your packaging.
Amazon uses Product size tiers that calculate categories based on the unit weight, product dimensions, and dimensional weight of a packaged item.
This is helpful information to have if there is a question as to the measurements of your products.