Hello manukeo,
I have been working on pathfing intensive game myself and saw your post as I was searching for clues.
I noticed that if you use a big layout, regenerating obstacle map takes long time. But with small layouts, it's very fast. If you could break down your levels into smaller chunks, it may help. Otherwise, you are stuck as I am. But ashley has a to-do-list which includes partial obstacle map regeneration, which will hopefully solve our mutual problem. Unfortunately, my game doesn't work with smaller layouts, hopefully yours will.
The entity-based regeneration of obstacle map is under works I believe.
About the re-start with old map issue, I am fairly sure you can fix it with your events. Restarting has some tricks to it, I am sure you are skipping a line or sth. Just regenerate the map on restart and it should fix.
About enemies outside view sleeping, it really seems smaller layouts are your ultimate solution. But you shouldn't worry about enemies outside your view dropping performance. If it's an issue, just don't create them untill player aproaches close to them.
Hope you keep working on your project.
Regards;
-Wind.