Hi Christian,
                    Thanks for quick response. 

will following serializing xquery help to generate the Doctype and xml declaration?

Original XML file:
===================
<?xml version="1.0"?>
<!--
Configuration file for user test suite.
 -->
<!DOCTYPE testSuiteConfig SYSTEM "../../../configs/TestConfig_2_1.dtd">

<testSuiteConfig version="2.1">
    <testSuiteEnv>
        <paths>
            <path type="input" value="../data"/>
        </paths>
.......

<Basex Database Name>/<folder name>/<xml file name>.xml:  XML file in Basex Database:
============================================================================
<!--
Configuration file for user test suite.
 -->
<testSuiteConfig version="2.1">
    <testSuiteEnv>
        <paths>
            <path type="input" value="../data"/>
        </paths>
.......


Can I run following xquery to get original XML file. 

XQUERY:
========
declare namespace output = 'http://www.w3.org/2010/xslt-xquery-serialization';
declare option output:method 'xml';
serialize(<Basex Database Name>/<folder name>/<xml file name>.xml ,
map {
    'method' : 'xml'
     'xml' : map { 'doctype-system' : '<!DOCTYPE testSuiteConfig SYSTEM "../../../configs/TestConfig_2_1.dtd">',  'omit-xml-declaration' : 'no' }
    }
)

Above serializing xquery will help to generate the Doctype and xml declaration. 
Thanks,
Srikumar

From: Christian Grün <christian.gruen@gmail.com>
Sent: Tuesday, July 28, 2020 9:27 PM
To: Srikumar Choudhury <schoudhu@opentext.com>
Cc: James Ball <basex-talk@jamesball.co.uk>; BaseX <basex-talk@mailman.uni-konstanz.de>
Subject: Re: [EXTERNAL] - Re: [basex-talk] BaseX 9.4 - XQuery locks - documentation query
 
Hi Srikumar,

As document type definitions and XML declarations are not part of the
XML information set, they are not stored in the database. However, you
can easily recreate them when serializing your documents. See [1] for
further information.

Hope this helps
Christian

[1] https://urldefense.com/v3/__https://www.w3.org/TR/xml-infoset/__;!!Obbck6kTJA!OZeMfuu_v5bg2MlWBgvOV5Cz4kfvZzejlmLdia84fV9ScLMuUO5R91AP4AVy7d0PwQ$
[2] https://urldefense.com/v3/__https://docs.basex.org/wiki/Serialization__;!!Obbck6kTJA!OZeMfuu_v5bg2MlWBgvOV5Cz4kfvZzejlmLdia84fV9ScLMuUO5R91AP4AWXSI7EQA$



On Tue, Jul 28, 2020 at 5:49 PM Srikumar Choudhury
<schoudhu@opentext.com> wrote:
>
> Hi,
> <!DOCTYPE some name SYSTEM .. and <?xml version="1.0"?> data loss are happening while importing the xml document using db:replace(...) API.
>
>  <?xml version="1.0"?>
>
> <!DOCTYPE testSuiteConfig SYSTEM "../../../configs/TestConfig_2_1.dtd">
> etc.
> We need help to resolve this issue.
> we are using Java executeQuery api of XQExpression. class to run "db:replace(...)" query to store document in Basex database, but while retrieving the XML files from basex server we notice data loss. we can loss above data.
>
> Please help us, how we can resolve this issue or share some documentation, which can help to resolve this issue.
>
> Thanks,
> Srikumar