Omer Hecht of Catlabs, who deal in Jobo parts for the USA, says to mix a cup of food grade citric acid in warm water and fill the water bath.
Leave it overnight circulating (or even over the weekend if needed) to remove the deposits: it won't hurt the hoses or pump. In fact, it will probably help, as gunk tends to build-up on the pump impeller in in the housing, causing premature pump failure.
I used the last packet of Jobo Systems Cleaner on my ATL 2200 and let it circulate 12 hours at 100 degrees Fahrenheit (roughtly C41 bath temp). After that I turned off the pump, let it set overnight and recirculated the same bath for 6 more hours before dumping it and flushing with 3 changes of water.
My circulation pump improved flow quite substantially and the tub and hoses look like new.
I got the above advice from Omer when I asked for a subsitute for the Jobo Systems Cleaner. He said to use the Citric Acid just the same way as you would the Systems Cleaner.
Hope this helps...