I have set a theme for this webform project in the web.config file and also a masterpagefile
<?xml version="1.0" encoding="utf-8"?><configuration><system.web><pages theme="themeName" masterPageFile="~/mp1.master" /></system.web></configuration>
Unfortunatly this did not work. I have spend a long time searching why my application kept showing the old masterpagefile. I believe that it had to do with this checkbox:
When you publish your webform application and click on configure, you should set the checkbox near the ‘allow precompiled site to be updatable’.
Otherwise it seems that during the compilation, it will bake in the configured masterpage file in your *.aspx files.
Please let me know if I am wrong, but this did fix it for me.
Good luck!