I did some further testing and I think it's very likely that I completely misjudged the situation. I looked at the logs and saw the same pattern in the logs, but without the associated ~45% packet loss. Then I looked closer and figured out that these logs actually don't indicate flapping links, but occasional connection losses on eth0 and the attached PC going to WOL on eth1. These looked to me like flapping because that could explain the packet loss and the ERL was powered on for so long that there were a LOT of these lines in dmesg. I also did a memtester run over 360MiB RAM, which turned up nothing, so I don't believe it's a memory issue. Sorry for the inconvencience!
So now I'm waiting for the next time I get packet loss to do some further debugging. Is there a good way to determine the source of packet loss on ERLs? Connection setup is ERL eth0 -> short ethernet cable -> Thompson DOSICS modem -> ISP. I can ping the ISP backbone router from my (different) internet connection without any packet loss, so the problem lies somewhere between the ERL and the ISP backbone. A restart or the ERL fixes the problem, but I'm not certain the ERL causes it.