Getting the error "Cannot add or remove items from Newtonsoft.Json.Linq.JProperty" in Json.net

Assuming Values is a List<MyObject> and your MyObject class looks like this:

class MyObject
{
    public string Time { get; set; }
    public int Level { get; set; }
}

you can replace all that code with the following to get the result you want:

string json = File.ReadAllText(fileName);
Values = JToken.Parse(json)["docs"].ToObject<List<MyObject>>();

This works because Json.Net will ignore missing properties by default. Since the MyObject class does not contain an _id property to deserialize into, you don't need to jump through hoops trying to remove it from the JSON.

Explanation of why Remove() didn't work

JToken.Remove() removes a JToken from its parent. It is legal to remove a JProperty from its parent JObject, or to remove a child JToken from a JArray. However, you cannot remove the value from a JProperty. A JProperty must always have exactly one value.

When you ask for token["_id"] you get back the value of the JProperty called _id, not the JProperty itself. Therefore you will get an error if you try to call Remove() on that value. To make it work the way you are doing, you'd need to use Parent like this:

if (inner["_id"] != null)
    inner["_id"].Parent.Remove();

This says "Find the property whose name is _id and give me the value. If it exists, get that value's parent (the property), and remove it from its parent (the containing JObject)."

A more straightforward way to do it is to use the Property() method to access the property directly. However, this method is only available on JObject, not JToken, so you would either need to change the declaration of inner to a JObject or cast it:

foreach (JObject inner in token["docs"].Children<JObject>())
{
    JProperty idProp = inner.Property("_id");
    if (idProp != null)
        idProp.Remove();
    ...
}

Lastly, as mentioned in the comments, if you're using C# 6 or later you can shorten the code a bit using the null-conditional operator:

    inner.Property("_id")?.Remove();