In fact, the surface used to define the "General Section" for BEAM elements is not transfered to the new model with command "FILE > MERGE". Please report the problem to FEMAP developers at the Solution Center GTAC Siemens PLM Software
As a workaround, use command "FILE > EXPORT > FEMAP NEUTRAL" and import the resulting *.neu file in a new session of FEMAP.
This has been fixed and will be in the upcoming FEMAP v11.1.2 maintenance release. Expect v11.1.2 in the next week or so.