Using mnemosyne 2.3.6 in a headless environment, I set the user/password in the following manner:
$> cd /path/to/mnemosyne-data-directory
$> python
>>> import sqlite3
>>> conn = sqlite3.connect('config.db')
>>> c = conn.cursor()
>>> print c.execute('select * from config where key like "%remote%"').fetchall()
[(u'remote_access_username', u"''"), (u'remote_access_password', u"''")]
>>> c.execute('update config set value = "YOUR PASSWORD" where key = "remote_access_password"')
<sqlite3.Cursor object at 0x7f6bc9916ab0>
>>> c.execute('update config set value = "YOUR USERNAME" where key = "remote_access_username"')
<sqlite3.Cursor object at 0x7f6bc9916ab0>
>>> conn.commit()
>>> conn.close()
>>> # just an extra check to see the file was written.
>>> conn = sqlite3.connect('config.db')
>>> c = conn.cursor()
>>> print c.execute('select * from config where key like "%remote%"').fetchall()
[(u'remote_access_username', u'YOUR USERNAME'), (u'remote_access_password', u'YOUR PASSWORD')]
>>> conn.close()
When I start mnemosyne (mnemosyne -d /path/to/mnemosyne-data-directory and try to connect a client, using the username and password set fails. When inspecting the keys set in the sqlite db, they have returned to empty strings. Syncing a client with an empty username and password works as expected.
I cannot reproduce this when editing config.db manually with sqlite browser. After starting and stopping the headless server, the username and password are still in the config file, and syncing with those values works. Are you sure you're not confusing directories/files?