I've encountered this problem a few times from workaround, but it keeps coming back. I have no idea how I solved it initially, but now the problem has persisted for quite some time.
What I want to do:
Is to have my player and weapons all in one .blend, and to let the player switch out weapons, whereby a given weapon is added or deleted whenever a weapon change occurs.
This is requiring the weapons to be in a separate layer. Linking object doesn't seem to support this. I've tried using different groups for each set of assets, but that also did not appear to do anything.
Picture related, the groups I am referring to in game. Any help is greatly appreciated. I can provide additional information if necessary.