The problem you're experiencing is likely a desynchronisation between NCrunch's in-memory model and the codebase you're working in.

It's fairly rare, but sometimes when performing many refactoring and/or search/replace actions it can show up.

The causes of desync issues are not yet understood. The appear so rarely and randomly that tracing them is almost impossible. I have a theory that they are being caused by race conditions between the manner in which VS is reporting the changes to NCrunch, and the updating of VS's internal buffers.

Usually the desync will affect one file in a project - although the build problems won't usually make it clear which file this is. The failures tend to appear around the dependencies of the affected file, rather than on the file itself. Simply making a text change to the file (i.e. adding a blank space somewhere) will resync the engine and allow it to continue without a full reset needed.

Sorry, I wish I could offer an immediate solution to this one ... but we do need to find a way to reliably catch it in order to kill it. Do let me know if you manage to find any pattern to the changes you make that surface it.

There are some design changes I may be able to make in the hope that they will resolve the problem in future. I'm keen to hear if it goes away or improves when you update Visual Studio.

V1 was plagued with many problems like this. Over time, they do get solved.