I know this is a crazy old thread and OP has likely moved on -- but in case anyone else like me is searching for the "servers are out of sync!" error and finds this as the only question...
I had this issue and figured out a solution that worked for me and thought I'd share. In my case, I think I must have accidentally tried to recompile with the server still running which caused a whole kerfuffle that made the server not have a clean exit. "./athena-start stop" seemed to be working fine, but the servers were still technically running.
I ran "ps -ef | grep ragnarok" ("ragnarok" is my server user, so this may be different if you created an alternate name). This is what I saw even though my server was stopped:
ragnarok@revitaro-backend:~/Hercules/conf$ ps -ef | grep ragnarok
ragnarok 13489 18634 0 17:09 pts/1 00:00:00 ps -ef
ragnarok 13490 18634 0 17:09 pts/1 00:00:00 grep ragnarok
root 18632 18612 0 14:43 pts/1 00:00:00 sudo su ragnarok
root 18633 18632 0 14:43 pts/1 00:00:00 su ragnarok
ragnarok 18634 18633 0 14:43 pts/1 00:00:00 bash
ragnarok 22159 1 0 00:41 ? 00:00:15 ./login-server
ragnarok 22160 1 0 00:41 ? 00:00:13 ./char-server
ragnarok 22161 1 0 00:41 ? 00:01:44 ./map-server
ragnarok 23383 1 0 14:56 pts/1 00:00:01 ./login-server
ragnarok 29904 1 0 15:32 pts/1 00:00:01 ./login-server
Note the 3 processes for "./login-server" and the instances for "./char-server" and "./map-server" -- those are the problem children.
I killed them one by one using their process IDs (second column from the left).
ragnarok@revitaro-backend:~/Hercules/conf$ kill 22159
ragnarok@revitaro-backend:~/Hercules/conf$ kill 22160
ragnarok@revitaro-backend:~/Hercules/conf$ kill 22161
ragnarok@revitaro-backend:~/Hercules/conf$ kill 23383
ragnarok@revitaro-backend:~/Hercules/conf$ kill 29904
I cleaned it up a bit -- but while running these the servers started emitting their standard shutdown messages (the ones you normally see with ./athena-start stop).
After doing this and a new configure packet ver, "make clean", and "make", my server worked normally again. Hopefully this helps someone else!