My Mint is based on Debian, and your Mint is based on Ubuntu, but I will guess that these panel actions work the same because we are both using Cinnamon desktop.If I click on them when my window has disappeared, another new window is opened, and the old window is not available
For example, let's work with one at a time... start with Thunderbird (it's on my panel too). Start with everything closed. Click the Thunderbird panel icon... and it should open up. Click on the panel icon again, and it will minimize Thunderbird. Click the panel icon again, and it opens up the same Thunderbird... not a new instance. Whether Thunderbird is minimized or visible on the desktop, you should still see that faint line below the Thunderbird icon on the panel. I said earlier I thought it was white or gray, but it's almost certainly "Mint green" now that I think about it. That faint line below the icon only disappears when you actually close Thunderbird.
The File Manager should behave the same way. So should Opera (at least the 3 browsers I use behave the same way).