I imagine, since the rules have been deemed unlawful, the Premier League can't just retrospectively change them and punish Arsenal, Brighton etc. by apply market interest rates to shareholder loans.
But...
This also means that they can't punish other clubs under those old unlawful rules as then you are apply one rule for one club (Man City, Newcastle etc) and not another.
So...
You have to "disapply" all the APT rules and start again, paying compensation to those impacted by the enforcement of the unlawful rules in the first place.