When you do this it's a good idea to split the system at an anchor for this very reason. Sometimes, in large systems, you may even want to BUILD an anchor at a convenient point for splitting the analysis. Intermediate anchors in very large piping systems are usually required anyway, simply to provide control points in case of failures.

If you choose to have a big, floppy piping system, then in addition to entering displacements, you also need to enter rotations at your split. Most fatigue problems are caused by bending stresses, and rotations have a lot more to do with that, in most cases, than displacements.

Finally, you need to make sure you have entered the data correctly. If you have messed up units, or switched coordinates, you could easily have created your own mess.