I’m running into the same issue. Since 4.25 it seems impossible to create variables with the “User” Domain inside modules.
I had for example a custom module for calculating global and local wind influence. Till 4.25 my module provided the needed User Variables (that get filled with data from Blueprints) correctly named and automatically linked with this module. So every artist creating a System that needs to be influenced by our Wind Sources only had to add this module, and everything was set up automatically.
Now with 4.25 the module can’t provide the user variables anymore, that are communicating with the Blueprints. That means the artists have to create all the User Parameters again and again for every System that has this module included and name them correctly, so that Blueprints don’t lose the linking. This is really dangerous for bigger projects where more than one artist is working on VFX.
Funnily enough, the modules were updated correctly when upgrading to 4.25. The modules I created before 4.25 kept their user variables and still provide them to the systems. However, the variables are no longer editable, there is no option to create new one, and it causes a lot of crashes in 4.25, so I assume that this approach is no longer consistent with Epic’s philosophy on how to handle user variables in Niagara. I hope that in the future they will implement a way to provide and link user variables via modules again for the reasons mentioned above.