Lost custom settings on User App

I've just renewed a signed certificate in my User Application keystore (userapp.keystore), but when the server reboot all the theme preferences we had changed have been lost.

We have User App 3.6.1 on linux and use jboss as the web server. The logos had been changed to match our corporate branding, and have been working quite happily for 2 years. The organisational signed a certificate for us, and this was now up for renewal.

My steps were;
create a new signing request.
Import new chained cert into userapp.keystore.
restart server.

Thats all I changed but when I reboot the settings were back to the default Linen profile.

Any ideas why this happened and if I can get the custom branding back??

thanks