Tips for using this buggy addon:
0. Deal with it.
Ok, 1. Organize with folders or folder trees instead of tab trees when you're working with a big chunk of tabs for maximum safety. Never ever should you make blank tabs (about:blank, new tabs, or blank pages) father of other tabs. Definitely gonna f up your tree after a restart if you spot buggy behaviors with tabs before it. This one is on Firefox.
2. You may often encounter scrambled up tree structures and missing tabs that are actually hidden after a restart, so you might want to have "expand all trees" in your context menu to make them reappear, or enable expanding trees with double click. This alternative doesn't always work though.
3. Use a session restore addon that saves and restores tab metadata 'by nature', just in case everything is beyond redemption. You might already be using one anyway so this tip goes the last.