Edit: After re-reading your comment now I realized that I had probably misunderstood it. It seems to me that you request a functionality to remove "dead" bookmarks.

As I had already replied to a previous comment requesting this, I had already played with such checks. But there are so much inherent difficulties (URLs responding in nonstandard ways, temporarily delayed, replying only when certain context strings are sent, etc.) that this would require a lot of fine-grained configuration options to work properly, and it would completely shift the focus of the extension. Also, it would require permissions which IMHO are not appropriate for the extension.

There are other extensions specialized only on such checking. I recommend to use these instead.

It is the first time that somebody reports such a problem; I was not able to reproduce it.

Edit:

Now bookmarkdupes 4.0 is out. Internally, this is a major internal rewrite, so it might have fixed your problem.

If the problem should persist, I would appreciate if you open a bug on github (or if necessary write me an email) so that we can discuss technical details.

Edit:

The current version on GitHub now experimentally opens in a tab instead of a panel and displays bookmarks as clickable URLs. If the experiment is successful it will be released as version 4.0