I was experimenting with editing the installed world file to remove unroutable terrain. That part of the experiment worked (see
http://www.den.simlogical.com/denforum/index.php?topic=1207.0 ). So of course I had to remove the store protection
Then someone said don't use the decrapifier, use s3rc to unprotect it. So I did that and no longer had the problem with disappeared pipes. From my point of view that solves my problem, but I was interested in what lay behind it anyway.