I have a sessionTimeout for my project like this
<cfset this.sessionTimeout = "#createTimeSpan(0,5,0,0)#">
for some reason pages on a deeper level inside of other folders are timing out before the 5 hours within like 20 minutes... Do I need to insert this in all application.cfc's to make it work correctly? I thought they all trickle down from the top level.
Unless you are extending the previous Application.cfc, or possibly using the same application name, your previous setting will no longer exist. You could also increase it in the CF Admin to make it global.