I'd suggest first trying to restore the original server.crt from backup if possible. If you cannot do this, then the below command should allow you to create a new one:
This needs to be run from the directory: "%\ProgramFiles%\Symantec\Symantec Endpoint Protection Manager\apache\bin"
openssl req -config ..\conf\ssl\openssl.cnf -new -x509 -out server.crt -key ..\conf\ssl\server.key
After this, just copy the "server.crt" file from the "..apache\bin" folder to the "..apache\conf\ssl" folder, replacing the server.crt file that has apparently become corrupted. You can always rename the original first if you want to be safe.
Finally, restart the services.
#EDIT#
Oh yeah, it's worth mentioning that you'll be asked for certificate attributes like location, common name and stuff after hitting return on the above command