Phil,
Sorry for the vague description. What I meant was when I remove the FEM, the laminates that I have made available for things such as the PRSEUS skin, stringer web, and flange web, are lost. This might be related to the same issue causing the loss of the failure modes. I just checked and it looks like only the laminates are lost (any available isotropic materials remain).
The main challenge is that my component numbers change (e.g., number of wing ribs changes), so for each iteration I have to push my new components into the appropriate groups. I was hoping that everything else would remain unchanged.
Thanks,
Trevor