Hi,
it's difficult to point you to the right direction without knowing more details about the problem. I suggest to check the following:
- what are the applications impacted? (all the apps / specific ones)
- only some sources/destinations or all the traffic?
- are the apps slow or simply not working?
- does the problem happen when reloading both central WAE's or just one of them?
after you narrowed down the issue, you might want to look into a specific area to troubleshoot on. Here you have a good starting point:
http://docwiki.cisco.com/wiki/Cisco_WAAS_Troubleshooting_Guide_for_Release_4.1.3_and_Later
You might want to look into the "Troubleshooting WCCP" section of that document.
Depending on your findings you might also need to grab sys-reports from the WAE's involved and tcpdump on core/edge location.
hope this helps,
Fabrizio