1. please keep in mind that the 1-D bar elements only have axial stiffness (and strength).
2. Normally, the influence of the differing material properties at the welds is negligible compared to other effects, or at least it can be simply taken into account by setting the reinforcement material in the model to the worse of the "normal" (original) and "welded" steel properties.
3. If you think this is not the case for your analysis, please explain + send some sketches (see also ATENA Troubleshooting, 2.1.1; the document is included in ATENA installation and also available for separate download from our web under Products - ATENA - Documentation).