I did a lot of digging yesterday using mcedit and nbtexplorer. It would seem that havocx42's tool is indeed migrating the buildcraft pipes correctly. The issue appears to arise when the converted world is started for the first time.
To simplify my testing I edited my buildcraft config to match pre and post migration. I then used havocx42's tool such that it didn't know about the buildcraft.genericpipe id. It did however know about the internal pipe id conversion. For clarity all buildcraft pipe blocks (be they wood, gold, transport or conductive) all share the same block id (166 in my case). And in the minecraft nbt files this blocktype has an internal variable that stores what kind of pipe it is. With this set up I checked the pipes data using mcedit before and after using Midas. Both showed that the block id was the same, and that the internal pipeid variable had changed as per my mapping. After starting the world the pipes were still invisible. So I fired up mcedit again. This time although the block id was still the same, all the internal variables had been deleted.
At this point I've run out of ideas. If starting the map is causing the invisible pipes I'm just going to set the block id to air and refund the people on the server their pipes. Apologise and ask them to rebuild