If your system works, you have no need to read this. You won't hit this issue, it's already fixed. If your system is unable to update, or you have schadenfreude, read on.
Sorry. My bad. Very recently some changes were pushed to Pentoo which moved the Pentoo Overlay from /var/lib/layman to /var/db/repos, for a few reasons, none of which are hugely relevant (although one of them was to make gpg verification work). When this was done, it passed a test case on my system, and was pushed without extensive testing. As such, a few issues popped up, all relating to stupid mistakes made my me personally.
I may have caused the following depending on how unlucky you were:
If your system is refusing to sync with an ugly backtrace about missing pentoo.asc
If your system says the profile is invalid.
If /usr/sbin/pentoo-updater is a dangling symlink to nowhere (command not found)
All of this is properly handled and fixed with the latest pentoo-updater, which you should be able to easily enough get by following these directions:
If you have /var/db/repos/pentoo:
1. cd /var/db/repos/pentoo
2. git pull
3. ./scripts/pentoo-updater.sh
4. everything should work now
If you have /var/lib/layman/pentoo:
1. cd /var/lib/layman/pentoo
2. git pull
3. ./scripts/pentoo-updater.sh
4. everything should work now
If this isn't enough to get you out of the hole i dug, please open a bug on the issue tracker and you will receive help.
https://github.com/pentoo/pentoo-overlay/issues
Respectfully,
Zero_Chaos