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In order to help you as quickly as possible, before clicking Create Topic please provide as much of the below as you can. Feel free to use a pastebin service for logs, otherwise either indent short log examples with four spaces:
example
Or for longer, use three backticks above and below the code snippet:
longer
example
here
Some or all of the below information will be requested if it isn’t supplied; for fastest response please provide as much as you can 
Nextcloud version (eg, 12.0.2): 15.0.12
Operating system and version (eg, Ubuntu 17.04): Ubuntu 16.04.6
Apache or nginx version (eg, Apache 2.4.25): Apache 2.4.18
PHP version (eg, 7.1): 7.3
The issue you are facing:
Cannot access some files in web interface, nor sync in client.
About one week ago the sync client started to complain about "File or directory not found: " of one of my directories. I can see/open the files both on my laptop as well on my server (directly accessing /nextcloud/user/files/…). I have also not modified the files since after I installed Nextcloud, and user and permissions are same as for other files.
If I try to access the directory from web interface the “loading circle icon” will rotate forever.
If I try to access the file on my iphone client app I immediately get “Request failed: not found (404)” error.
In the desktop client it looks like this:
I have tried occ files:scan without any difference.
My thought is that this directory reference for some reason has gone missing from the database. If someone have had same experience or can lead me in some direction, please help!
Is this the first time you’ve seen this error? (Y/N): Yes
Steps to replicate it:
Don’t know
The output of your Nextcloud log in Admin > Logging:
No particular error in this log.
The output of your config.php file in /path/to/nextcloud (make sure you remove any identifiable information!):
config.php
$CONFIG = array (
'instanceid' => 'xxxxxxxxxxxx',
'passwordsalt' => 'xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx',
'secret' => 'xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx',
'trusted_domains' =>
array (
0 => '192.168.1.215',
1 => 'localhost',
),
'datadirectory' => '/nextcloud/data',
'overwrite.cli.url' => 'http://192.168.1.215',
'htaccess.RewriteBase' => '/',
'dbtype' => 'mysql',
'version' => '15.0.12.1',
'dbname' => 'nextcloud',
'dbhost' => 'localhost',
'dbport' => '',
'dbtableprefix' => 'oc_',
'dbuser' => 'xxxxx',
'dbpassword' => 'xxxxxxxxxxxxxxxxxxxx',
'installed' => true,
'memcache.local' => '\\OC\\Memcache\\APCu',
'mail_smtpmode' => 'php',
'mail_smtpauthtype' => 'LOGIN',
'maintenance' => false,
'theme' => '',
'loglevel' => 2,
'log_rotate_size' => 10485760,
'enable_previews' => true,
'preview_max_x' => 1024,
'preview_max_y' => 1024,
'twofactor_enforced' => 'true',
'twofactor_enforced_groups' =>
array (
),
'twofactor_enforced_excluded_groups' =>
array (
),
'updater.release.channel' => 'stable',
);
The output of your Apache/nginx/system log in /var/log/____:
From access.log when trying to access directory:
192.168.1.112 - - [03/Oct/2019:22:34:10 +0900] "PROPFIND /remote.php/webdav/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git HTTP/1.1" 404 616 "-" "Mozilla/5.0 (iOS) Nextcloud-iOS/2.24.1"
No error messages in error.log.
Here is sync log from Nextcloud client (2.5 for linux) after doing a forced sync:
client sync log
[_csync_detect_update Database entry found for xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git, compare: 1522149914 <-> 1522149914, etag: 5aba2a1af292c <-> _invalid_, inode: 0 <-> 3413553, size: 0 <-> 0, perms: fd <-> fd, checksum: <-> , ignore: 0, e2e:
[_csync_detect_update file: xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git, instruction: INSTRUCTION_EVAL <<=
[OCC::AccessManager::createRequest 6 "PROPFIND" "https://xxxxxxxxxxxxxxx/remote.php/dav/files/hans/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git" has X-Request-ID "83ee2b79-d223-41fd-b1a5-9dac69d2d490"
[OCC::AbstractNetworkJob::start OCC::LsColJob created for "https://xxxxxxxxxxxxxxx" + "/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git" "OCC::DiscoverySingleDirectoryJob"
[OCC::WebFlowCredentials::slotFinished request finished
[OCC::AbstractNetworkJob::slotFinished QNetworkReply::NetworkError(ContentNotFoundError) "Servern svarade \"404 Not Found\" på \"PROPFIND https://xxxxxxxxxxxxxxx/remote.php/dav/files/hans/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git\"" QVariant(int, 404)
[OCC::WebFlowCredentials::stillValid QNetworkReply::NetworkError(ContentNotFoundError)
[OCC::WebFlowCredentials::stillValid "Error transferring https://xxxxxxxxxxxxxxx/remote.php/dav/files/hans/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git - server replied: Not Found"
[OCC::LsColJob::finished LSCOL of QUrl("https://xxxxxxxxxxxxxxx/remote.php/dav/files/hans/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git") FINISHED WITH STATUS "ContentNotFoundError Servern svarade \"404 Not Found\" på \"PROPFIND https://xxxxxxxxxxxxxxx/remote.php/dav/files/hans/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git\""
[OCC::DiscoverySingleDirectoryJob::lsJobFinishedWithErrorSlot LSCOL job error "Error transferring https://xxxxxxxxxxxxxxx/remote.php/dav/files/hans/Dokument/xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git - server replied: Not Found" 404 QNetworkReply::NetworkError(ContentNotFoundError)
[OCC::SyncEngine::handleSyncError ERROR during csync_update : "Fil eller mapp kunde inte hittas: xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git"
[OCC::ActivityWidget::addError Item "Dokument" retrieved resulted in "Fil eller mapp kunde inte hittas: xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git"
[OCC::ActivityListModel::addErrorToActivityList Error successfully added to the notification list: "Fil eller mapp kunde inte hittas: xxxxxxxxxxxxxxxxxxxxxxxxxxx/.git"
[OCC::SyncJournalDb::close Closing DB "/home/hans/Dokument/._sync_9629db275513.db"
[OCC::SyncEngine::finalize CSync run took 37642 ms
[OCC::Folder::slotSyncFinished Client version 2.5.2git Qt 5.9.5 SSL OpenSSL 1.1.1 11 Sep 2018
[OCC::Folder::slotSyncFinished SyncEngine finished with ERROR
[OCC::Folder::showSyncResultPopup Folder sync result: 2
[OCC::Folder::slotSyncFinished the last 4 syncs failed