Sorry for delayed response, I just wanted to make sure I synced up with the other team(s) and people that were involved with this incident to get a better understanding of what is going on.
When you create the version in WMX or in ArcGIS, it is a snapshot of the data at the point. If you open 2 instance of ArcMap containing a layer from the database where the version was created and modify/add/delete a record in one of the ArcMap instances, the second ArcMap instance you have opened does not know of the change made synchronously. It has to be refreshed or the data needs be reloaded in ArcMap for the changes to be visible in the second map document.
This is a behavior for any version in ArcMap and there is refresh tool on the versioning toolbar in ArcMap that handles this scenario.
This is exactly what is going on when you load data through the ArcCatalog window while in a Workflow Manager - ArcMap session. There is no way to automatically synchronize the records that you have loaded into the version. You will have to use the same tool on the versioning toolbar to refresh the version in order to see your updates. Alternatively, you can use a GP tool to load the data as part of the workflow before running the open ArcMap step. The other option is to run the workflow within ArcMap after you have finished loading your data. This last option will repoint the layers to the version and will ensure that any changes that were made earlier is visible in your map session.
I have spoken with the Aeronautical solution team and they will update documentation or the Task Assistant Workflow shipped with the template to address this situation.
I hope this helps explain the situation better.