Paying the loan charge does not resolve the underlying tax dispute with HMRC

[interestedparty]

I have open inquiries for years between 2012-2018, but repaid my overdrawn capital account balance before 5th April, 2019.

HMRC have notified me that these inquiries still need to be resolved.

I understand, and accept this, but wouldn't repaying the overdrawn capital account be the resolution to these inquiries, based on the assumption that the basis of these inquiries purely related to the overdrawn capital account?