You can add filters, groups, order, as much as you want, because each will return an IEnumerable (some methods return a child interface, like Order, which return an IOrderedEnumerable).

Then, you consume this this enumerable, most of the time with a foreach (procedural, or LINQ style, and will consume the enumerable), where you can update the values.

In the end, it's still C#: you can add side effects, where you want, even in the select, even if you shouldn't.

Most of the times, "when it tends to make this kind of query difficult" you can just consume your query with a foreach, and do the rest with the procedural style.