On Linux, file names that start wit a dot (“.”) are equivalent to hidden files. If you type “ls” or “ls -l” for a short or long listing of files, you will not see any files that start with a dot. If you type “ls -a” hidden files will be shown as well. I guess this is nothing new. At least it may help you to locate any files that start with a dot (“.”).
There have been reports nextcloud overwrites .user.ini and .htaccess at times:
You could download nextcloud fresh and extract in a different directory and copy the missing files across.
Alterntatively, here is a trick to update the file scan:
(do this only if you are sure of your “.htaccess” file integrity)
Edit your “config.php” and include the following line:
‘integrity.check.disabled’ => true,
Now reload the page and when you see the yellow banner click on ‘rescan’.
Log-out and next time you log-in as admin you will not see the banner.
You can now delete the line you put in your config.php to re-enable the integrity check, and you will not see the banner anymore.