I'm running into what I believe to be a bug in Arcgis Pro. I'm using 3.4 with both of the most recent patches installed, but I think this bug might go back to just 3.4. The issue I'm having is when I use the Add Join tool in model builder. Within a model I am joining a polygon layer to a table off a common field. The initial running of the model will work, but after the first run it will change the polygon layer to a layer file instead of pointing to the location of the layer on my network. Once it changes it to a layer file the tool no longer runs because it says the layer does not exist. I have created many models like this one with past versions of Pro and they all worked fine, and ones that were created on older versions of Pro continue to work on the most recent version. I've included a screenshot of the model to show how my polygon layer is showing as a nonexistent layer file instead of the location of the layer.
This is the only publically facing bug for Add Join and Pro 3.4
I would report it in case it is specific to modelbuilder
I think this sounds more like BUG-000169420 - "ArcGIS Pro ModelBuilder input variables are un-sourcing when running after upgrade when the input variable references a file path." It was first seen at ArcGIS Pro 3.3.
The workaround is to add layers to the Contents pane and use the Input Variable drop-down menu to add these to the model. Currently this bug is under review.
In Product Plan as of Wednesday
The issue has been added to the development team's backlog. The goal for issues with this status is to address them in a near-term release (next release or two). Check the issue's Additional Information or Alternate Solution section to see if there is helpful information until it can be fully addressed.
So 3.5 is in internal Beta... I wonder if it is on the radar.
Thank you both for your responses. I'm using these models as scheduled geoprocessing tools. My workaround was to set the inputs as parameters. When I set up the scheduled tool I'm able to put the source layers as the parameter inputs. This seems to make the model 'hold' the source layer as the input.