Suppose I have two smooth projective varieties $X$ and $Y$ in $\mathbb{P}^n$, that intersect along a smooth subvariety $Z$. Is there a formula to compute the degree of the join variety $J(X,Y)$ of $X$ and $Y$? Of course if $Z$ is $\emptyset$ then we have the classical formula, but what if $Z$ is non-empty?



Join of two intersecting varieties
You can find a lot of material on the intersection theory of join varieties (including all that I write in this answer) in the conference paper [2] of Flenner. At the end of the second page (p.130) you find the statement of the general formula for the degree of joins:
$$\deg X \deg Y = \deg V + \deg \pi \deg J,$$
The notation is as follows:


* $X,Y\subseteq \mathbb P^n$ are projective (irreducible) subvarieties, over an arbitrary field $K$;
* $V$ is their Vogel-cycle, which is a special cycle supported on $X\cap Y$;
* $J\subseteq \mathbb P^n$ is their embedded join;
* $\pi:\tilde J \to J$ is the (rational) projection from the abstract join $\tilde J\subseteq \mathbb P^{2n+1}$ of $X$ and $Y$.


This formula is a consequence of the correspondence principle of van Gastel [3] and of the intersection theory of Stückrad and Vogel [4]. Remarkably, it is valid regardless of the dimension of $J$. 
The paper of Flenner also explains how to express the Vogel-cycle (and so also the degree of $J$) in terms of Segre classes, cf [1]. 


1. Ådlandsvik B.: *Joins and higher secant varieties*. Mathematica Scandinavica (1987) 61:213-222.
2. Flenner H.: *Join Varieties and Intersection Theory* pp.129-197. In: Ellingsrud G., Fulton W., Vistoli A. (eds) *Recent Progress in Intersection Theory.* Trends in Mathematics, Birkhäuser 2000.
3. Gastel, L.J. van: *Excess intersections and a correspondence principle*. Inventiones Mathematicae (1991) 103:197–221.
4. Stückrad J., Vogel, W.: *An algebraic approach to the intersection theory* pp.1-32. In: *The curves seminar at Queen's Vol II*. Queen's papers in pure and applied mathematics No.61, Kingston 1982.


