The short answer, explained
An HMRC enquiry doesn't end just because correspondence stops, or because you feel you've answered everything HMRC could reasonably ask. It formally ends only when HMRC issues a closure notice, a document that states either that no amendment is needed, or exactly what amendment HMRC is making and why.
In practice, most enquiries close through negotiation: you and HMRC reach an agreed position on the facts and figures, and HMRC then issues a closure notice reflecting that agreement. If you disagree with HMRC's conclusions, you can still ask for a closure notice reflecting HMRC's position, then appeal it.
If HMRC seems to be taking an unreasonably long time without progressing matters or explaining why, the law gives you a way to force the issue: applying to the First-tier Tribunal for a direction that HMRC issue a closure notice within a specified period.

