I routinely use a 5-10% citric acid solution (in water) where I work to remove rust from small samples so I can examine fracture surfaces.
I wouldn't leave the solution in the system any more than an hour. Even that may be too long. Citric acid is a mild acid that can removes corrosion without much affecting the base metal. But if left too long, it can start corroding healthy metal like any other acid. This is speaking from experience where I forgot about my samples and left them in solution overnight.
Ultrasonic cleaning in the solution - as I use in the lab - "melts" the corrosion off the surface. Unfortunately, we don't have that luxury with our cooling systems.