A flat file schema can be configured to generate empty elements for empty content
– using the “Generate Empty Nodes” option.

It seems that at runtime, the flat file dissasembler can generate “<foo></foo>”
for these empty nodes in cases where “Validate Instance…”
in the IDE would have generated “<foo/>”.

Where this can cause pain is if you receive a message like: “<foo><bar></bar></foo>”

into your orchestration, and then do a series of assignments like:

xmlDocVariable = myMessage;
// xmlDocVariable2 initialized because xmlDocVariable is needed for other things...
xmlDocVariable2.LoadXml(xmlDocVariable.OuterXml);
myMessage2 = xmlDocVariable2;

At this point, myMessage2 is going to be the serialized representation of xmlDocVariable2. 
By default, you will now get:

<foo>
..<bar>
..</bar>
</foo>

Notice you now have carriage returns, line feeds, and spaces (shown here as periods)
involved.  Depending on how you now go after /foo/bar, this can be bad (i.e.
you won’t get empty content when you might expect it.)  You can avoid this
behavior by doing:

xmlDocVariable2.LoadXml(xmlDocVariable.OuterXml);
xmlDocVariable2.PreserveWhitespace = true;
myMessage2 = xmlDocVariable2;

Thanks to Tomas and Carlos for
setting me straight on PreserveWhitespace – I was trying to set it before the
call to LoadXml, and this doesn’t work.  Never a dull day in BizTalk land…

The documentation
for PreserveWhitespace is a little strange.  This functionality would seem
to be better represented as parameters to Load/Save, rather than as a property…

“If PreserveWhitespace is true before Load or LoadXml is called, white
space nodes are preserved; otherwise, if this property is false, significant white
space is preserved, white space is not.  If PreserveWhitespace is true before
Save is called
, white space in the document is preserved in the output; otherwise,
if this property is false, XmlDocument auto-indents the output.”