New gentoo-bashcomp version loop all files in /etc/portage/repos.conf (old version only *.conf files).
This is a good thing but can be skip backup file (~ ending file)? This can cause an issue, see 
A solution is list files ending with a character with '/etc/portage/repos.conf/*[a-zA-Z]'.
Removing the backup file also solved this issue for me, thanks.
This leads to completion errors in various tools after deleting a repo with eselect-repository.
$ equery uses <TAB> bash: cd: /var/db/repos/snapd: No such file or directory
bash: cd: /var/db/repos/snapd: No such file or directory