When the update completes I get a warning about “packages not in AUR”. They include a bunch of Endeavour related packages such as brand theming etc.
What is the problem here?
It sounds like you overwrote your /etc/pacman.conf. Did you merge pacnew files and overwrite it?
One quick way to fix this is to overwrite with a clean copy from here:
https://raw.githubusercontent.com/endeavouros-team/EndeavourOS-ISO/refs/heads/main/airootfs/etc/pacman.conf
That did it ! Thanks. Dunno how it got over-written but it obviously did.
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You must have done it yourself by using pacdiff (from the welcome menu) because it does not happen automagically. Be careful with those pacnew files. Only if you are sure it is safe to overwrite the original file do so. Take a good look at what is inside in the pacnew file and compare it with the content of the original file. Just meant as a friendly warning. 
That’s good advice. Still finding my way around EndeavourOS. I really like this distro. Thank
Being based on Arch, you will find a wealth of information on Archwiki. On the specific subject of .pacnew files, if you are interested: https://wiki.archlinux.org/title/Pacman/Pacnew_and_Pacsave
Wow! Now I think I understand the routines. Still curious as to how pacman.conf got replaced by a new file without the proper repositories. I will have to re-read the info in that link. Thanks for the follow-up.
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Think this happened in this particular case because it was a update coming from the arch repositories. So therefore the EOS repositories where not known by Arch, something like that.
The same thing could have happened with other arch based distributions I think.
That is highly strange. The very purpose of creation of a .pacnew is to prevent such an event.
Yes like I said earlier this doesn’t happing automagically, we had a number of users in here that did overwrite the file by probably using pacdiff for this purpose.