When trying to update a model using the Spatial Join option in ModelBuilder, the model is not updating as expected.
This is likely related to the elements involved being outside of the tolerance assigned in ModelBuilder. You can try adjusting the tolerance value in ModelBuilder. However, this issue may also be related to the source file being on a different coordinate system or scale. Based on that, if the source file is a shapefile or DXF file, try adding this as a background layer. If you do a Zoom Extents, you may see that the source file is not near the model data. If that is the case, adjust the source file coordinates to line up with the model data and the issue should not occur.
How to populate or updated an existing model with GIS-IDs
Using Modelbuilder to import external data