Waiver worry

Three years ago company Z started to repay the loans and interest but the interest waivers were overlooked and the last three accounts show a disparity in the loan capital balances and that a higher sum is due to A.
Following an HMRC enquiry the interest amounts were re-calculated and the correct loan accounts were restated in the following accounts. However HMRC are claiming that the additional sum ostensibly due to A (due to the additional interest accrued) gives him control and makes X an associated company. If correct significant additional tax will arise on X due to the loss of marginal relief.
My view is that the parties' always intended that they would be on equal terms. I think TA 1988 s 416(2)(c) supports our contention that any distribution of assets must follow the actual legal entitlement and not that which has been...