Java Web Dynpro applications do not appear in the user Theme (branding).
After patching java webdynpro applicatins are not picking customize themes. It is picking sap_tradeshow theme.
It creates the below CSS URL
As per my understanding, it should pick the URL something like below
sap-cssurl = https%3A%2F%2Fportal.customer.net%3A443%2Firj%2Fportalapps%2Fcom.sap.portal.design.urdesigndata%2Fthemes%2Fportal%2Fcustomer%2Fur%2Fur_ie6.css%3F188.8.131.52.1&sap-cssversion=184.108.40.206.0
I have also checked the Web Dynpro property useWebDynproStyleSheet which set to false.
We patched to SP16 from NW 7.01.SP13
It is corrected by applying the latest patch level of EPPSERV SCA file.