If the search function in your Mail App does not work or your marked messages shown properly try this:
- Close Mail App
- Copy and paste the following code into terminal and execute:
sudo defaults write /Library/Preferences/com.apple.security.appsandbox \ UnrestrictSpotlightContainerScope -bool true
Works fine with me. All my marked messages appear again and I can search all my mails properly.
Let me know in the comments if this helped you.