Contract settlements: contents
You should check the other guidance available on GOV.UK from HMRC as Brexit updates to those pages are being prioritised before manuals.
The guidance about contract settlements at EM6000+ only relates to direct tax. You must never include VAT or VAT penalties in a contract settlement
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EM6001General
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EM6001aDeeds
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EM6002Settlement Discussions
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EM6003Overcoming Delay
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EM6005Calculation of interest: Contents
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EM6050Calculation of penalties: Contents
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EM6100Surcharge: Contents
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EM6200Expected Offer: Contents
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EM6300Letters of Offer: Contents
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EM6400Acceptance: Contents
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EM6411Post-Settlement Issues: Contents