When the Data Model is Regenerated, it is built and then compiled using a “Temp” location and then the Data Model is written to the Database. As an AppServer starts, the Data Model is pulled out of the Database and it is written into the Server\Assemblies directory.
You should not be manually moving any files into the Assemblies directory unless installing a hotfix.
Check out a previous post on this topic: Adding UDField - Procedure - #6 by Rich