Looking at your logs, I would say that the RE CPU has been consumed by some task, leading to the scheduler slips, and then failure of L2 control protocols - I notice that apart from LACP flapping, your spanning-tree topology also changed at the same time, which may be indicative of BPDUs not being sent or processed in a timely manner:
Jun 7 01:42:53 sw-cloud-ex3300-stack eswd[10087]: Root bridge in context 0 changed from 4:cc:4e:24:3a:e9:b8 to 8192:84:b5:9c:46:79:01
Check for any core dumps, but unfortunately without more logs you probably aren't going to get very far with root cause on this one