actually, the changes to the trees don't persist at all! the python script above is probably a better bet.

CORRECTED VERSION 

@Vladyslav are you able to remove the previous version? I can't.

function removeDups() {
    // if DON'T do this, could end up deleting whole subtrees when you only mean to delete the node
    $('#expandAllButton').click();
    urls_list = [];
    urls_set = new Set();
    tonodes = $$('#savedtabundefined');
    tonodes.forEach( (node) => {
        let url = $('.nodeTitleContainer',node).href;
        urls_list.push(url);
        urls_set.add(url);
    });
    console.log(tonodes.length + " tabsoutliner tabs");
    console.log(urls_list.length + " url occurrences");
    console.log(urls_set.size + " distinct urls");
    if(tonodes.length == urls_list.length) {    
        removed_dups = 0;
        kept = 0;    
        dups_with_children = 0
        // keep the last occurrence of a url, and remove the rest 
        last_occurrences = new Map();
        for(let i=urls_list.length-1; i>=0; i--) {
            let url = urls_list[i];
            if( last_occurrences.has(url) ) {
                if( $$('ul>li',tonodes[i]).length == 0 ) {
                    removed_dups++;
                    // tonodes[i].remove();
                }
                else {
                    dups_with_children++;
                    kept++;
                }
                // 
            }        
            else {
                kept++;
                last_occurrences.set(url,i);
            }
        }
        console.log(dups_with_children + " duplicates with children were NOT removed.");
        console.log(removed_dups + " duplicates with no children were removed.");
        console.log(kept + " tabsoutliner tabs were kept.");
    }
    else {
        console.error("Expected number of tabsoutliner nodes to be equal to number of url occurrences. This was false, so stopping to be safe.");
    }
    // undoes expand all
    $('#expandAllButton').click();
}
removeDups();

I'm sorry! There might be a race condition where the expand all button (which I thought would prevent that) doesn't work fast enough. 

I'll just modify it to never delete tabs with children. 

Only removes duplicates based on exactly matching URLs. Keeps the most recent occurrence. 

Here's a script to remove duplicates. There's also a list where you can put strings that, when found in the title of the tab, will cause it to be deleted, regardless of whether there are duplicates.

USAGE:

Bring TabsOutliner to the front.

control+shift+j (windows/linux) or command+shift+j (mac) to open the Developer Tools.

Click "Console"

Copy paste the code below into the line with the cursor. Press enter.

// if DON'T do this, could end up deleting whole subtrees when you only mean to delete the node
$('#expandAllButton').click();
first_occurrences = new Map();
urls_list = [];
urls_set = new Set();
tonodes = $$('#savedtabundefined');
tonodes.forEach( (node) => {
    let url = $('.nodeTitleContainer',node).href;
    urls_list.push(url);
    urls_set.add(url);
});
console.log(tonodes.length + " tabsoutliner tabs");
console.log(urls_list.length + " url occurrences");
console.log(urls_set.size + " distinct urls");
if(tonodes.length == urls_list.length) {    
    removed_dups = 0;
    kept = 0;    
    // keep the last occurrence of a url, and remove the rest 
    for(let i=urls_list.length-1; i>=0; i--) {
        let url = urls_list[i];
        if( first_occurrences.has(url) ) {
            removed_dups++;        
            tonodes[i].remove();
        }        
        else {
            kept++;
            first_occurrences.set(url,i);
        }
    }
    console.log("Removed " + removed_dups + " duplicates.") 
    console.log("Kept " + kept + " tabsoutliner tabs.");
}
else {
    console.error("Expected number of tabsoutliner nodes to be equal to number of url occurrences. This was false, so stopping to be safe.");
}
// undoes expand all
$('#expandAllButton').click();