I don't think you'd have any unsafe attributes, but if you can, find out if you need more than 1 bottle before adding it. Me personally I want to get every single bit (or as much as physically possible) of the flush out of the cooling system. So you'll want to do a thorough flush, but as for harming, the only thing I can think of is that you may not get all of the deposits out and they would stay in suspension in the coolant.
I don't want to give you any "OK's" and then something happen, but I have never heard of any harm coming from using the chemical, if you read the instructions it's obvious that you won't get all of the chemical out when using Prestone's method. How do you plan on flushing the cooling system?