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Easy solution is to leave permanent entries intact (to skip).
More sophisticated and potentially fruitful approach would be to reset from neg cache only entries that were updated in files.
Steps to Reproduce:
[nss]
filter_groups = root
filter_users = root, admin
$ id admin
id: ‘admin’: no such user
-- as expected, user 'admin' is filtered out
$ adduser test
$ id admin
uid=1389800000(admin) gid=1389800000(admins) groups=1389800000(admins)
-- user is not filtered anymore.
Initially reported as: https://bugzilla.redhat.com/show_bug.cgi?id=1824323
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