Presently, you should always disable NCrunch before updating your Nuget packages.

We've been trying for years to find an acceptable way to handle Nuget's package update system, but what seems at face value to be a rather simple system to handle is actually not simple at all. This has much to do with the inconsistent and asynchronous way that the updates cascade through the file system and VS structure. Given the state of affairs I have to say that it looks unlikely we'll ever be able to support Nuget package updates with the engine enabled.

We want to.

Detecting when it starts turns out to be quite simple.

Detecting the end of it is much, much harder. We haven't found an acceptable way to do this. So for now, we simply ask to make sure you disable the engine before you update packages.

I've also been bitten by this quite a few times and have learned to disable Ncrunch before the upgrade (though I normally only remember half way through!) I think an option for Nuget to automatically disable when detecting a nuget upgrade would be useful even if re-enabling isn't practical. Nuget can end up in quite a broken state when this occurs and I often end up fixing up csproj and packages.config files by hand.