EF database-first is very under-tooled in many places. Similarily to your problem, if you generate a model from DB and rename a column in CodeSpace (so column users.col_chr_UsrName is just User.Name), you also would lose it when regenerating the model.
If I remember well, in EF3, EF4 and even in EF5 there is no way to preserve them. If you just "update" the model, they have a chance of surviving, but regenerating never preserves anything.
You can try to create a script or set of scripts that you will run after regenerating, and those scripts may seek and apply fixes to the generated model. But thats, well, "workaround" (literally, work and around), not a real solution.
Another thing, with more work, is to define Views or StoredProcedures (or custom table mappings) that will handle the projection, but they sometimes also may get hairy after regenerating (especially custom table maping which will always evaporate).
You can actually ignore the unwanted columns and prepare a set of light LINQ wrappers/accessors that will perform the projection, and put them in some static MyTables class and use that class instead of RawTable. That will work and may be usable, but is not again pretty.
IMHO, the best approach is to use either a script that will fix the model afterwards, or live with the unwanted columns, or .. not use the autogeneration from within the designer. Try to find another, more smart, generator.