Recently I have had a few questions come in regarding pdm_configure resetting the web_cgi_url, or the default repositories' Upload Paths. The good news is that we have TEC documents to address both of these issues!
For the web_cgi_url issue, please see http://www.ca.com/us/support/ca-support-online/product-content/knowledgebase-articles/TEC502617.aspx
For the Upload Path issue, please see http://www.ca.com/us/support/ca-support-online/product-content/knowledgebase-articles/TEC1608229.aspx
If there is anything else that we can add or clarify for you, please comment below!