Hope I'm not stirring an existing topic
I stumbled upon this "bug" yesterday (I've read FFF-351 that mentions how to operate pipe connections with existing fluids): I have this big oil processing base that requires tremendous amounts of water (currently three pumps). When I noticed I had to increase the water flow, as I tried connecting a new water pump to the existing water pipe bus, I had the error "cannot mix different fluids".
Obviously I wanted to add water in water pipes. I didn't try flushing because I knew there wasn't any mixing happening.
I also tried to disconnect an existing pump and reconnect it to its network, I had the same error.
What worked was to let a robot install the pipe to connect the pump to the water network, and it would gladly do it without errors.
I'm running a few mods (EvoGUI, the fat controller, long reach, Ingos advanced start, ToDo list, FNEI, if my memory serves me correctly), but they don't really touch the fluids system. I do use the Squeak Through mod (https://mods.factorio.com/mods/Superche ... %20Through), which could have a potential influence.

