To relight the scene, press 'alt L' while in the world editor. This will make the buildings the correct color. There's no reason why only your logs wouldn't save. Maybe you're not saving correctly (just do file > save....) though this will overwrite your normal port town mission file, which i suggest you backup.
-EDIT-
I've had requests for people about building a jail. Here's the script to do it:
*NOTE* if you don't understand what i say below, do NOT try to do it!
Just add the code below into a blank space (like line 4) of your 'main.cs' file (it's in your root aot folder.)
*Note*: replace the blank in setTransform("_____________"); with coordinates to where your jail is.
If you don't know how to get the coordinates of where your jail is, i suggest you don't try this at all.
Once you've added the code, launch AoTv3 and open the GUI editor. Add 2 buttons to the adminGUI menu (just copy and paste an existing button) and make the command for the first button commandToServer('jailPlayer'); and for the second button, change the command to commandToServer('unjailPlayer');. Click Apply. If you don't know how to do this, don't try it.
*NOTE* the following script was made completely by me (rudyman). I worked hard to get it to work.
function serverCmdJailPlayer(%client)
{
%clientguy = %client.getControlObject();
%victimx = lstAdminPlayerList.getSelectedId();
%victim = %victimx.getControlObject();
%cname = %clientguy.getShapeName();
%vname = %victim.getShapeName();
$vpos = %victim.getTransform();
%victim.setTransform("_____________");
%victim.isTimeout = 1;
messageClient(%victimx, '', '\c3You have been jailed by %1!', %cname);
messageClient(%client, '', '\c3You have jailed %1!', %vname);
messageAll("", '\c3%1 was jailed by %2.', %vname, %cname);
}
function serverCmdUnJailPlayer(%client, $vpos)
{
%clientguy = %client.getControlObject();
%victimx = lstAdminPlayerList.getSelectedId();
%victim = %victimx.getControlObject();
%cname = %clientguy.getShapeName();
%vname = %victim.getShapeName();
%vx = getWord($vpos,0);
%vy = getWord($vpos,1);
%vz = getWord($vpos,2);
%victim.setTransform(%vx SPC %vy SPC %vz);
%victim.isTimeout = 0;
messageClient(%victimx, '', '\c3You have been released by %1!', %cname);
messageClient(%client, '', '\c3You have released %1 from jail!', %vname);
messageAll("", '\c3%1 was released from jail by %2.', %vname, %cname);
}