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You can also find the tree data in plain text (JSON format) in the File System folder of the Chrome Profile. Again, some Next version will allow to import such files back. It can be done even now, but the procedure is somewhat complex...

One other solution, and maybe better - export the tree in HTML through Ctrl-S. Programmatically deduplicate the file - and import it back in the fresh instance with empty tree by drag and dropping the hierarchies (next version will allow to import the whole tree by dragging the root node, current one have a bug that prevent this).
well, just check the DOM structure. You can run any automation in the tree from the chrome developers console.

I plan a new release on the next week. It will not fix this problem meantime, but some next release shortly after it - will. The real solution is not in removing duplicated but not to have them in a first place
This is the result of the "Continue Where Leave off" option enabled in the Chrome settings. Tabs Outliner currently conflict with it. The solution is or disable it or open some empty Chrome window (so it will get all the tabs from a previous session) before reopening any windows with tabs from Tabs Outliner - if this is a first regular window (tabs outliner window is not considered "regular") .
Cannot reproduce this issue, can you mention your Chrome version and OS?
Unfortunately, a mobile browser does not support extensions.
But soon there will be an upgrade wich will regularly back up the tree to google drive and a mobile application or just a web interface to access and view such backups from mobile browser
I will check it. It will be a good reason to start support Opera oficcialy.
I am actually cannot reproduce it nor on Windows nor on Ubunta, sorry.
Yes, not something to be proud of.
This is actually not the Tabs Outliner data but more like Java Script virtual machine garbage, that is actually garbage collected by Chrome when they need more ram. Through i myself regularly restart TO because of this issue. For 50 000 nodes the number is same actually. 
Version with much better memory usage planned to be released in 2 months.
Where did you reading so? 
I cannot find any API that allow restoration of tab history.
Very strange issue. 
Is this problem persist after complete Chrome Exit (through the Exit menu item)?

Can you please post here the content of the chrome://version/ page.

This is clearly abnormal, it must react on double click. but if not, and you need to reopen them you can try Ctrl or Shift clicks on saved tabs, as they rendered using HTML links this must reopen them in new Chrome windows. Or you can save the tree to HTML file throgh Ctrl-S (save as complete html) and reopen from it.