IfModule Mod_rewrite - settings in .htaccess file not retained during upgrade

Hello, Every time I upgrade I have to re-enter the IfModule Mod_rewrite settings in my .htaccess file. I'm sure this is a miconfiguration I have somewhere but not sure where. Any ideas? See info below.
thanks!

Steps to reproduce

  1. Occurs After each Upgrade
    2.
    3.

Expected behaviour

.htaccess file should retain info

Actual behaviour

.htaccess file does not retain info and has to be added back into .htaccess file after upgrade

Server configuration

Ubuntu 16.04

Web server:
Apache
Database:
Mysql

PHP version:
PHP 7.0.22
ownCloud version: (see ownCloud admin page)
10.0.5
Updated from an older ownCloud or fresh install:
Update
Where did you install ownCloud from:
Package installation
Signing status (ownCloud 9.0 and above):

Login as admin user into your ownCloud and access 
http://example.com/index.php/settings/integrity/failed 
paste the results into https://gist.github.com/ and puth the link here.

No errors have been found.

The content of config/config.php:

Log in to the web-UI with an administrator account and click on
'admin' -> 'Generate Config Report' -> 'Download ownCloud config report'
This report includes the config.php settings, the list of activated apps
and other details in a well sanitized form.

or 

If you have access to your command line run e.g.:
sudo -u www-data php occ config:list system
from within your ownCloud installation folder

*ATTENTION:* Do not post your config.php file in public as is. Please use one of the above
methods whenever possible. Both, the generated reports from the web-ui and from occ config:list
consistently remove sensitive data. You still may want to review the report before sending.
If done manually then it is critical for your own privacy to dilligently
remove *all* host names, passwords, usernames, salts and other credentials before posting.
You should assume that attackers find such information and will use them against your systems.

<?php
$CONFIG = array (
'updatechecker' => false,
'instanceid' => 'xxx',
'passwordsalt' => 'xxx',
'secret' => 'xxx',
'trusted_domains' =>
array (
0 => 'xxx',
1 => 'xxx',
2 => 'xxx',
),
'datadirectory' => '/var/www/owncloud/data',
'overwrite.cli.url' => 'https://xxx.net',
'dbtype' => 'mysql',
'version' => '10.0.4.4',
'dbname' => 'xxx',
'dbhost' => 'localhost:3306',
'dbtableprefix' => 'oc_',
'mysql.utf8mb4' => true,
'dbuser' => 'xxx',
'dbpassword' => 'xxx',
'logtimezone' => 'UTC',
'installed' => true,
'mail_smtpmode' => 'smtp',
'mail_smtpsecure' => 'ssl',
'mail_from_address' => 'owncloud',
'mail_domain' => 'xxx',
'mail_smtpauthtype' => 'LOGIN',
'mail_smtpauth' => 1,
'mail_smtphost' => 'xxx',
'mail_smtpport' => '465',
'mail_smtpname' => 'xxx',
'mail_smtppassword' => 'xxx',
'files_external_allow_create_new_local' => 'true',
'maintenance' => false,
'loglevel' => 0,
'memcache.local' => '\OC\Memcache\Redis',
'filelocking.enabled' => 'true',
'memcache.distributed' => '\OC\Memcache\Redis',
'memcache.locking' => '\OC\Memcache\Redis',
'redis' =>
array (
'host' => 'localhost',
'port' => 6379,
'timeout' => 0,
'dbindex' => 0,
),
'theme' => '',
);

List of activated apps:

If you have access to your command line run e.g.:
sudo -u www-data php occ app:list
from within your ownCloud installation folder.

Are you using external storage, if yes which one: local/smb/sftp/...

Yes, Local

Are you using encryption: yes/no

No.

Are you using an external user-backend, if yes which one: LDAP/ActiveDirectory/Webdav/...

LDAP configuration (delete this part if not used)

With access to your command line run e.g.:
sudo -u www-data php occ ldap:show-config
from within your ownCloud installation folder

Without access to your command line download the data/owncloud.db to your local
computer or access your SQL server remotely and run the select query:
SELECT * FROM `oc_appconfig` WHERE `appid` = 'user_ldap';


Eventually replace sensitive data as the name/IP-address of your LDAP server or groups.

Client configuration

Browser:

Operating system:

Logs

Web server error log

Insert your webserver log here

ownCloud log (data/owncloud.log)

Insert your ownCloud log here

Browser log

Insert your browser log here, this could for example include:

a) The javascript console log
b) The network log 
c) ...

Hi,

You can enable this module with a command like this, witthout writing it in the .htaccess file

a2enmod "module" enable