Unexpected Second Instance of SQL Started
It turns out - when reviewing all the logging that I could, that the Windows Event Log has a crash of SQL recorded - however, SQL itself has no crash in its logs, and the log wasn't closed and a new one created as you'd expect when SQL restarts.

In our monitoring, the second instance never grows beyond 2gb of RAM - and the RAM usage itself never grows, but the pagefile grew at 11gb per day.

I can't see the cause of the crash, and I'd probably have to open a Microsoft support ticket to see why it crashed, created a new instance, but never closed the existing instance - never released it from being the instance as the service, and never died or took over that I can see.

We can see some timeouts for a minute from an API that talks to the server, but no "unavailable" messages.

It seems like the crash is the underlying cause - but that's as far as I can determine for now, and it seems unusual to me.

None of our monitoring, or our consultants monitoring picked up the crash.