You should not deploy any dlls with your app that are already included in mojoPortal because then you risk deploying incorrect versions. ie your post build event should not copy any dlls except those from your own projects and other dependencies that are not used in mojoPortal.
In the case where you depend on the same dlls as mojoPortal, if you have a problem you should drop the reference to the dll and then add it again, then delete the dll from the Web/bin folder and rebuild the solution so it pulls the new version in from the _libs folder.
We recently changed to a newer version of NeatUpload in version 184.108.40.206 and then again to a newer version in 220.127.116.11. In both cases I had to change the references for my add on products Form Wizard Pro and Web Invoice Pro to the new version and recompile. That is why I made a new release of Form Wizard Pro and Web Invoice Pro corresponding to the new 18.104.22.168 release of mojoPortal. They must depend on the same version of NeatUpload. There are other ways to fix version conflicts such as using assembly mapping from Web.config to map things that depend on the older version to the newer version. But that would require more steps from end users so I find it easier to just ship a new version of the add ons that depend on the same version of NeatUpload. It doesn't change very often, but it has changed a few times recently.
Hope it helps,