I recently had to re-install Chrome for a repair problem. It all went OK, except for my bookmarks. From an initial number of 1,800, after the re-install, I had 10,500 !
Bookmarks had been imported from Firefox and IE and added to those on Chrome. Out of 10,500 there were 8,700 duplicates. I used AM-Deadlink to sort it out. - http://www.aignes.com/deadlink.htm
So many duplicates spells a long and irritating time sorting it out. I found that AMD deleted 300 duplicates in 10 minutes, so 8,700 would take about 4.5 hours. I did a few short manual tests , which worked OK, then went for broke on the lot.
Click the desktop icon and AMD lists all your bookmarks. Click the "Find duplicates" icon and they are then shown with a primary arrow for the first one. Click the "Select all duplicates but one" and the whole list is blued except the primary bookmarks. Click the "Delete" icon and wait.
The only indication that the program is working is the flashing of the blue computer traffic light. Task Master says "Not responding" - rubbish, IT IS, ignore that, in fact do not use Task Master at all or you get a screen freeze and have to start again. Just WAIT.
My 8,700 did take about 3-4 hours. It deleted and reshuffled a few of my Bookmark Bar special items, but I soon found those I could remember using Bookmarks Manager and put them back resorted. No primary bookmark is lost, it may just have another name or be another duplicate to the one you have selected.
For small batches you can use a manual method. Click your first item, then hold down the arrow key above CNTRL and go to your last item and click it. All go blue. You have then to hold down the CNTRL key and scroll up the list clicking every primary item - the small arrowed ones. Do not release the CNTRL key until finished and DO NOT click any other space outside the scroll bar or you will have to start again.
The point of this post is to say what an excellent program AM-Deadlink is to control your bookmarks. Nothing is perfect, but you will do no better than AMD.
AMD also lists bookmark errors if required.