Bridge seems to be struggling to rate any new series of photos, why is this?

It's not uncommon for people to experience issues with folders containing large numbers of images. Is 1000 large? Well you could try working with a much smaller number to see how that affects things. Remember that Bridge has to build thumbnails and previews of all of these images and this all takes time depending upon the speed of your system hardware and the preview quality settings you have selected. 100% size preview generation in particular consumes resources.

As for deleted images, Bridge doesn't delete anything without being instructed to. Is this user error? I trust that you made a backup before doing anything else so that you are able to restore the missing images.