Hello, original link syntax:

/DisplayArticle.do?dt=<xsl:value-of 
select="java:bridges.framework.util.URLEncoder.encode
(internal-web-link/@dt)"/>&amp;
dn=<xsl:value-of 
select="java:bridges.framework.util.URLEncoder.encode( 
java:bridges.framework.util.StringUtil.replace( string
(internal-web-link/@dn), '?', '_') )"/>&amp;
cn=<xsl:value-of 
select="java:bridges.framework.util.URLEncoder.encode
(internal-web-link/@cn)"


would result in a link:

<a href="
/student
/DisplayArticle.do?dt=Education%20Link&amp;
dn=Discovery%20Online&amp;
cn=main">Discovery 
Online</a>

If the whitespace is being stripped then maybe the issue is 
the cariage returns??
Thanks!

> Our site generates several types of links via XSLT that 
> contain whitespace. My problem is that althought these 
> links are acceptable in a browser (whitespace is ignored) 
> they break in HTTrack resulting in an incorrect request.

Whitespaces are generally stripped by httrack in the 
begining & end os the link. Can you give more details, like 
the original html link syntax?