If you go to the Chrome Web Store (need Opera's Install Chrome Extensions as well) you can then download an app called Bookmarks clean up. It will allow you to delete duplicates, broken urls etc. Far easier than doing it manually.
@maticop You may have more luck if you ask in a Avast forum. Usually antivirus have ways to report false positives and even to set up folders and files that should not be checked.
@dankllamas Hey so I've been running through the same issue.
Solution: right click on one of the workspaces and click on Manage workspaces. You will see all of your workspaces and next to them a check icon. Uncheck and check back again the one that's not working and voilá. That worked for me