Just rust particles or is the water rusty brown in color also? You don't say much about your system. A water test should indicate, IMO, whether water chemistry only needs to be addressed or whether the system should be drained and new water, with appropriate chemical added at the same time.
Two examples in my experience with my 1000 gal used LP tank for water storage. I too cleaned it as best I could, but I knew unknown stuff still was in the tank. I added a high temperature water filter to my system and was fairly surprised at the quantity of stuff trapped by the filter. I changed it monthly for a period of time, and then as I noticed that it no longer was trapping much stuff, I lengthened the time between changes, and now I haven't changed it for over a year, as the last change showed nothing visible in the filter.
As to water chemistry and draining and refilling the system, since I had very rusty water, I decided to drain and refill the system, but first I had the water professionally tested. You can get a pretty good read on the quality of your water with a swimming pool test kit, showing pH, total alkalinity and hardness. The pH is very important, especially if less than 7.0. But there are other components of water that also are important. The general rules I follow are pH as suggested by mfr or if no recommendation, pH 8.5 to 11.0; total alkalinity in a range of 250-700, not hard or overly soft water, and chemical to scrub free oxygen out of the water. In my case the refill was essential because my well supply water was pH 6.5 (acid), and I refilled from another water source that showed pH of 7.0 (neutral).
After the professional testing I bought the quantity of boiler chemical suggested by the testing and treated the water with the refill. Ever since, several years now, the water has remained clear and the filter remains clean.
I don't have experience with more than one boiler chemical tester and supplier, that being precisionchem.com. There are others available and you can decide what you want to do.
