There are state regulations when it comes to water testing for NxStage Machines. In my case of NY, it was a monthly test. I swapped out more Pureflow CPU's than I care to think about in my year on Home Hemo, we tested monthly, and ultimately, I ended up on bags anyway. I don't know what state you livve in, but it is safe to assume that your clinic is bound by state regulations. It may just be coincidence that this is happening after a breakdown.
Water testing is a huge expense for clinics in NY. It should be drawn by a trained technician (which means a site visit to the home monthly). In many cases, it is more efficient for a clinic to just use bags exclusively. A storage pain - for me especially as I lived in a small NYC one bedroom apartment - but ultimately, it is to safeguard that we are not exposed to pathogens in our treatment.
I may have had a rant or two or three about my pureflow CPU
http://ihatedialysis.com/forum/index.php?topic=7743.msg113734#msg113734 BUT I have to say I loved it, and the simplicity of just making a batch over hanging bags and the aforementioned storage issues. But sometimes, we just have to play the game. It sounds like your clinic may have to figure out just what the proper protocols are to satisfy the unit, the manufacturer and the state. I hope that this all resolves for you soon Malibu.