In 6.1 updating the FEM took two steps:
1) In the HyperFEA application, you needed to use the "Pre-Process FEM" button. This pre-process split the FEM into several include files - PM, CL, CP, etc.
2) When sizing or analyzing the PM, CL, and CP files were written out for whatever components are active. The next time you ran the FEM the newly sized properties (in the PM1 include files) would be in the FEM.
You might be able to simulate a HyperFEA-like loop if you split the FEM into the necessary include files and then run a script that sizes the project and submits to FEA.
In 6.2 we added the concept of a separate "Update FEM" process that creates a brand new FEM from scratch - without a pre-pocess step and without sizing the project.