Using xmldom.writeToClob to update xml clob corrupts clob

Question

We are storing an xml document in a clob field in the db. As part of a data check we need to parse the xml and possibly remove a node. I can do that, and check the results using 'xmldom.writeToBuffer'.
When I try to write the data back to the db using 'xmldom.writeToClob' I get strange results. Data seems to be appended to the end of the clob and contains chr(13) characters at the end of each line.
Also does anyone know if the existence of whitespace in the xml clob would cause a parse/search to be slower?
I am new to xml and might be missing something fairly basic in the following code. Thanks in advance for any help.
Here is some of the code:
doc xmldom.DOMDocument;
curNode xmldom.DOMNode;
parentNode xmldom.DOMNode;
theNodeList xmldom.DOMNodeList;
str varchar2(4000);
begin
-- open xml_rec cursor (xml is the clob field opened for update)
-- Loop through all item elements
theNodeList := xmldom.getElementsByTagName(doc, 'item');
for m in 0..xmldom.getLength(theNodeList)-1 loop
curNode := xmldom.item(theNodeList,m);
--perform a check and possibly delete the current node
parentNode := xmldom.getParentNode(curNode);
parentNode := xmldom.removechild(parentNode, curNode);
xmldom.writeToBuffer(doc, str);
--I check the results here and everything looks good
xmldom.writeToClob(doc, xml_rec.xml);
--When I check the clob the data is incorrect.
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Answer 1

The next cod is a sample of the implementation xmldom.writeToClob used xmldom.DOMNode in the parameter of input.
DECLARE
XMLOut CLOB := EMPTY_CLOB();
XMLIn Varchar2(2000);
XSLPath Varchar2(2000);
BEGIN
DBMS_LOB.CREATETEMPORARY(XMLOut,TRUE); -- Give permit
DBMS_LOB.OPEN (XMLOut, DBMS_LOB.LOB_READWRITE); --open the file of read and write
XSLPath := '/users/gcardona/plantillas/report.xsl';
GE_BSXMLCONVERT.createElementName('COLUMN');
GE_BSXMLCONVERT.createElementAttribute('name', 'OUTXML');
GE_BSXMLCONVERT.addElement();
GE_BSXMLCONVERT.createElementName('table');
GE_BSXMLCONVERT.createElementAttribute('name', 'X1');
GE_BSXMLCONVERT.createElementAttribute('width', '100');
GE_BSXMLCONVERT.addElement();
XMLIn := GE_BSXMLCONVERT.toXML();
XSLTranform(XMLIn, XSLPath, XMLOut);--XMLOut is a variable in out in the procedure,
--here is where is return the file XML Process
insert into in_prueba (ID,XML_CLOB) values (200, XMLOut);
DBMS_LOB.CLOSE (XMLOut); -- Close File
DBMS_LOB.FREETEMPORARY(XMLOut); --free memory
GE_BSXMLCONVERT.clearMemory();
commit;
END;
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