I have a pipe network I created in a base drawing along with an alignment I created in the same drawing. I referenced that network into a bunch of sheets. Everything was fine. Then I had to change the name of the alignment in the base drawing, so I did. Now in all my drawings where the pipe network is referenced I get this message: "Reference alignment 'HRO-4 FINAL' not found in reference drawing" HRO-4 FINAL was the old name of the alignment. The alignment is still in the same base drawing, I just changed the name. The pipe network in the base is fine, it updated it's reference alignment to the new name. I recieve that message in all the drawings where my pipe network is dref'd.
Try removing the network reference from your plan, then recreate the data shortcut.
When creating the shortcut, there should be an option to "Override Reference Alignment".
Check this box and select the alignments new name.
We have run into a similar issue with this in our office. The way we dealt with this was to remove all references to the alignment in your pipe network in your base drawing then save and close the base plan. After this re-open the base plan and re-reference all your pipes and structures to the alignment. This should hopefully fix it.
Also, changing the reference alignment in the pipe network properties will not apply the reference alignment to existing pipes and structures in the network but will apply it to new parts added to the network. There is a free app on the app exchange that can quickly apply a new reference alignment to all the existign parts in a pipe network. http://goo.gl/2hUSwi
Hope this helps.
@Jason - When I try that, and then if I open the pipe network properties menu, the program crases everytime.