The mode flood is a desync or missing Uline issue which is bouncing services' modes. I am not sure what you mean, but chanserv *would* appear deopped to all people on 'other.server.im.not.on' (and servers connected under it) during the mode flood, until you (a 'legal' op on all servers) properly opped it.
Unless the servers have reported a different purpose for +o (in numeric 005) I can see no reason chanserv would not be opped after you opped it. Does /names #blah show chanserv as opped?