Deskzilla is not a full substitute for Bugzilla web interface. It addresses most of use cases and we're working on supporting every feature that you request. Yet the current version has limited functionality.
Currently, Deskzilla can download and handle effectively up to 40,000 bugs.
If you have more bugs in Bugzilla, that's ok unless you work with each and every bug. Use queries to download bugs only for your project, or only open bugs, or use whatever filter that defines which bugs you are working with.
If you need to work with more bugs anyway, give it a try. Deskzilla won't stop on bug number 40,001, though it may seem slower and require more memory. Meanwhile, we'll be working hard to push the limit into the sky.
Heavily customized Bugzilla installations are not supported. Deskzilla relies on some elements of Bugzilla web interface. If those elements are missing or changed beyond recognition, Deskzilla will fail to exchange data with Bugzilla.
Following is the list of standard Bugzilla features that are not supported by Deskzilla (as of version 2.1):
When you find out that you can't do something with Deskzilla, you can always press F9 and Deskzilla will take you to the bug's web page in Bugzilla. You have to be online, of course.
You are also welcome to request a feature that you need.