You could use the clonevm command and make a clone of the VM on an external or secondary drive. If you don't specify a snapshot and don't specify a mode then the current state configuration will be saved as the one and only state in the new VM. You then import the cloned VM into virtualbox.
The documentation is kind of confusing regarding the mode as it states "If machine is selected (the default), the current state of the VM without any snapshots is cloned." What this means is the cloned VM will not have the snapshot tree but it WILL merge all the snapshot VDIs into the base VDI (otherwise when you imported the new VM it wouldn't work).
For example, I had created a VM with two drives (C @ 50GB and D @ 250GB) and had about 30 snapshots where the data on drive D changed significantly between snapshots. My coworker needed a copy of the VM on his machine as well, but wasn't concerned about the snapshots. So I ran the following command:
VBoxManage.exe clonevm "D:\VirtualMachines\DevEnvironment\DevEnvironment.vbox" --basefolder "G:\CopyOfVM\" --options keepallmacs --options keepdisknames
Edit: Not sure if you have to give the full path to the VM as the docs say you just need to give a name (and I'm running come other commands so I cannot test right now). In this case that would just be: DevEnvironment
Note: No snapshot, mode or name specified so those all default. In this case "G" was an external HDD. You may not want those options. You especially should be careful with the second option (keepdisknames) in that, you'll have to remove the original VM before importing the clone.
In 4.2.10 (not sure about 3.2.14) you can delete intermediary snapshots between the current state and the first snapshot within the GUI and VBOX will automatically merge the differences between each snapshot. Sometimes you get errors if you ever did a restore and broke the "linear" tree, but you just have to delete any VDI in the Virtual Media Manager that is not attached to anything.
Hope this is helpful. Good Luck!