Larry,
 
The following guides provide information on command line aphelion exports.

Windchill Info*Engine® Installation and Configuration Guide
under Exporting Existing LDAP Directory Content
http://www.ptc.com/WCMS/files/28479/en/28479en_file1.pdf
 
The following guide has much more detailed information on Aphelion:
Aphelion Directory 2003.2 Administration Guide 
http://www.ptc.com/WCMS/files/29935/en/29935en_file1.pdf
 
The following guide has a section on backups:
Windchill System Administrator's Guide  
http://www.ptc.com/WCMS/files/29927/en/29927en_file1.pdf 
 
The key points you want to remember are
 
1.    Shut Down Windchill
2.    Do your Oracle Dump
3.    Do your Aphelion Export
4.    Start Up Windchill
 
Your backups will not be in sync if taken while Windchill is running.
 
I do not see how applying a maintenance release to a broken Windchill 
with an out of sync LDAP and Oracle would fix any issues, and I really 
couldn't comment on the issue unless I were to examine the logs on both 
systems before and after the update, it is unclear whether they were 
even throwing the same errors.
 
Thank you,
 
Ralph Goodwin
TSE
Technical Support Engineer
PTC
1-800-477-6435