Chrome being the best Browser out there IMO is still horrible at keeping and organizing Bookmarks! You can do things to Mitigate the issue, like not complicating the bookmarks that you save. I try not to have to many Folders Tiered. I also use many computers and sync them all, so when I make a change in one, I try to boot the others to get them up to date. If not, they will get messed up by all the complicated changes that have been made, chrome if just not good enough to keep up.
I did use a Bookmark manager at one time, but it is not supported anymore...Xmarks! It was quite good, and had many Tools to fix bookmarks in the cloud. I read that it was not supported anymore, but they are still noting it in reviews. Do a google search for "Best Free Bookmark Managers" and see what you can find. Just remember to back them up first.
Here is one HERE. Also, remember to turn off Chrome Bookmark manager if using a Third Party one, or else you will be into Duplicates up to your neck!
You can also look in Chrome Extensions to find more. Xmarks is still available there for some reason, perhaps it is still supported for a short amount of time?
hamluis has some good ideas with using some kind of file to find duplicates, wish he would elaborate on that.
I would research those bookmark managers and find one that will suit your needs. I'm stuck with Chrome for now as I just don't have the patience to find a new one that works the way I want it too.
You may want to clarify a little more because as bad as Chrome Bookmark Manager is I've got along with reasonably well.
(to the point where bookmarking extensions just crash when I attempt to sort them out).
I assume you mean Bookmarks just crash when attempting to sort them out? I don't know why this would happen, other than you have way to many and the structure is way to complicated for Chrome to handle. I had 2500 at one time, but think I have about 1500 now. Luckily I'm so sick of the situation I don't care if I loose them all LOL. I will endorse Xmarks as being very good, but you may want to find out how long it will be supported. You could use it just long enough to sort your stuff out, export and start over with Chrome.