How can I copy layers from one Synfig project to another without taking all the waypoints of those objects with it as well. I just want to have the layers from one project but not all the waypoints that go with it. Thanks for the help!
Also how can I delete all the keyframes and waypoints and object has? Do I have to go through and delete them all one by one?
Deleting a keyframe will delete the waypoints that might be on the keyframe.
To delete waypoints not on keyframes you have to delete them manually. You can do a trick. Encapsulate all the stuff that you want to clean the waypoints, then go to the created Paste Canvas layer and select the canvas parameter. It will summarize all the waypoints of all the parameters of all the child layers. ALT click one by one will erase all them.
Yes, it should be automatized. 
-G
You could also convert the channels to grey and back again. You then loose all waypoints on that channel.
Better choose “Disconnect” that will disconnet from the Animated Value Node and will connect to a new value given by the parameter at the time you do that action. But that’s tedious when you have many layers.
Yes, we need automatization 
-G
I noticed disconnecting on vertices only works on a vertex by vertex basis. I can disconnect a vertex but nothing happens when I disconnect the vertices list.
Yup, we could use little helpers here and there to do simple tasks that are done complex now. [size=85](Also we would need a selection box tool for the timeline and ability to select waypoints from different channels together.)[/size]
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Ah yes, in that case the Convert->Bezier List do the trick.
-G