Thanks spxza. I have had no luck with the flowing water update trick but will try a world anchor to see it that helps (it should if we are correct). I have also noticed that forcing a pipe-block update fixes it. In the process of replacing my pipes I replaced the "naked" pipe sections and then had to go up a level to continue. When I got upstairs and tore off the glass covers I had on the rest of the pipes (thus forcing an update of the pipe blocks themselves), everything went back to being A-OK.
Update: [[[ FIX ]]] I have confirmed in multiplayer v1.0.6 that using a dimensional anchor to keep chunks loaded prevents pipes from breaking. Broken conductive pipes-> place dimensional anchor to cover chunks in question-> remove and replace conductive pipes.
100% thanks go to spxza on this.