Updating AUR packages will have consequences for pacman

If you update aur packages with packer my recommend Aur tool, you should do

packer -Su

but if you have to realize that your pacman, the accepted Arch packages will also be updated. So if you have an issue with a certain package as I have now with libgl which interferes with the nvidia-utils
you should give the command the exception rule: packer -Su --ignore libgl
And don't forget to supervise the build process and act on warnings and possible additional dependencies.