ipsec-tools and tomoyo-tools are libre because doesn't needs be rebuilt against our kernels and headers to works well. This means Parabola's ipsec-tools-libre and tomoyo-tools-libre aren't needed anymore and it will be removed from repos.
You should install the ipsec-tools and tomoyo-tools packages manually using regular pacman methods. Accept the ipsec-tools-libre and tomoyo-tools-libre removal and that's it.