We are loading data from db:
var somethings = Context.SomethingSet.ToList();
Then someone deletes or adds rows outside of context. Out context still has caches deleted object, because it doesn't know they were deleted. Even if I call Context.SomethingSet.ToList(), our context still contains deleted objects and navigation properties are not correct.
What is the best method to refresh whole set from database?
The EF data context is an implementation of the Unit of Work pattern. As such, it is NOT designed to be keept around beyond the unit of work that is being done. Once your work is done, the expectation is that your data context is discarded.
This is a fundamental design decision for both EF v1, EF v4, and LINQ to SQL. Unless you have very specific data usage patterns and copious volumes of memory, you should avoid keeping your data contexts around longer than absolutely needed to complete your unit of work.