I had a copper chest that I'd upgraded to a filtered chest. I set a filter (in this case a whitelist for magical crops items and blocks) and everything was working fine. Then I upgraded the copper chest to a silver chest and noticed items were not being routed to the chest and not routed to any other available chest in the network of chests. I check the filter, it's been reset. I set the filter again, no change in behavior, I remove the chest, then place it again and set the filter again, still no change in behavior.

Was able to reproduce this, all chests are in the same chunk, this is in version 1.01

I think this is also fixed in the current dev version (same fix as the multi-chunk problem). The basic gist is: the tile doesn't get removed from the network when upgraded, even when it's not physically there anymore. The resetting filter is something I will look at now, should be an easy fix :)