Currently using Eagle ver 6.3, after almost 3 years.
The most pervasive difficulty (at basic level): a via is assigned to change layer during a rerouting; trying to delete it later is not allowed because Eagle considers it as part of the net (do it in the schematics, it says...!)
I recall deleting a via once after a sequence of wild attempts but could not repeat the series of events.
Ripping up was the solution. But to understand it I had to relearn how to properly change layers when rerouting (I was forcing vias instead of allowing Eagle to do it properly. Go figure.)