It dosen't matter if you consider your other tank to be way over filtered or not, because the BB colonies will only grow to a level that the food source will allow. I wouldn't touch the bio media in your other tank, or if you do, be very very wary of what could happen. You could end up with double trouble ammonia spikes.
Going off what you've said regarding taking the broken eheim bio media out of the equation, i'm pretty sure you will have an ammonia spike in that tank. You could do more water changes to keep it in check, using prime, which in itself will detoxify the ammonia for up to 48 hrs. Also, feed less and you could even try some of this bacteria in a bottle stuff that is being discussed on quite a few threads at the minute.
Either way, your BB colonies will eventually get back up to speed and things will settle down once more.