You can update the web_data.dat to set the WEB_CGI_URL value so that it is not reset after running pdm_configure.
Service Desk Manager 14.x and 17.x
All Supported Operating Systems
Update the web_data.dat file located in the NX_ROOT\data directory.
Change NX_WEB_HOST_REPLACE.
For example:
{ "1563", "WEB CGI URL", " http://NX_WEB_HOST_REPLACE/CAisd/pdmweb.exe", " http://NX_WEB_HOST_REPLACE/CAisd/pdmweb.exe", "web_cgi_url", "Installed" }