"As for the encounters, there is a weird thing I've noticed, unless the Encounter level is set to the level of the NPC and then manually lowered, nothing happens, i.e. Encounter default is level 1, all NPC's in the encounter are level 3, when the encounter starts they are level 3 still. But raising the default to 3 and then lowering it to 1, lowers it for all NPC's in the encounter. It also will raise all NPC's if you desire that."

Thanks I had figured that one out.
Glad to be able to continue creating the adventure with the current save. I did lose 2 hrs of work yesterday after I realized this was the case..doh!
Thanks for the help guys!