When the Flex Look and Feel theme is changed the Flex Master Page requires resetting because the Flex Master page becomes disabled. Your theme changes will be included in the default Flex Master Page once it has been reset.
This situation is caused by a change in how Microsoft manages 2013 sites. Please see this link for more information: https://technet.microsoft.com/en-CA/library/dn178510.aspx
When making a Theme Change in 2013 follow the instructions to change the Flex Master Page back to the “crmseattle.master” default settings. An IISReset is required at the end of these steps which will temporarily shut down all SharePoint sites.
Steps
- Logging into SharePoint as the Administrator and using SharePoint Designer point it to the address of your Flex sub-site – make sure the target is the Flex site and not the Top Level site. The example below in the red circle shows how the Flex site was addressed directly in this example.
- When you have successfully opened a connection to the Flex site, you will see a number of folder “Site Objects” on the left-side Navigation.
- Locate the Master Pages object and double click to open the list of current available Master Pages. The ONLY Master Page that is used by Flex is “CRMSeattle.Master”.
- Resetting the Master Page only requires that you “right click” on CRMSeattle.Master page entry on the list and change the following settings by clicking on them:
- Set as Default Master Page
- Set as Custom Master Page
- Once these changes are done you can close down SharePoint Designer.
- Next you will need to do an IISReset on the WFE Server to make sure these changes take effect (resetting Flex root site in IIS directly will have the same effect).