Fading particles and transition
I made a visualization a little like yours years ago, and used a similar technique, because it's the natural approach to the problem. After I spent a few years writing drivers for modern GPUs, I wouldn't use this approach at all, because it creates a dependency from one frame to the next, which introduces pipeline stalls and/or false sharing.

Today, I'd keep the path of the particle as part of its state, and render the whole trail each frame, instead of reusing the old FBO. It's conceptually a little more difficult, and you have to be careful that the way you draw the past path is exactly the same each frame. For example, if you represent the path with some kind of cubic spline, you can't just move the final control point forward, because it'll change the whole curve slightly. A circular buffer of (x, y) positions would be much easier to get right.

What you get in exchange for this extra complexity is (a) reduced frame time, memory use, and power consumption (which might be important if you're on mobile), and (b) you won't have your current problem at all. Maybe the frame time advantage won't be as big in WebGL, because you'll end up doing extra work in Javascript, which is slow, but memory bandwidth is more of a bottleneck on most systems. Just make sure that the co-ordinates you store are in the space of your simulation, and transform them into screen co-ordinates when you draw them, just like you would with a 3D scene.