It's better to ask now than to run into issues, so don't worry about this.
I had copied a bunch of files from Datastore1 to Datastore2 previously using the Datastore Browser, but I can delete all that to free up the space. Then I will have a full 500GB Datastore2.
Not sure what exactly you've copied, but since we are going to clone the virtual disk, the source will always be available in case the clone doesn't work as expected. So you can free up the disk space on Datstore2.
Do I just right click on the VM and choose something from the dropdown?
Yes, right click and select Remove from Inventory.
Am I doing this from SSH?
Yes, it's a command line tool. Also remember that it will run for quite some time due to the file size, so please remain patient.
Do these copy over as part of the clone process you mentioned previously?
No, that's why I have this step on the ToDo list. The vmkfstools command will only take care of the virtual disk (.vmdk) files.
I can just do this using the Datastore Browser?
Yes.
Again in Datastore Browser?
Again, Yes.
continuum said he was going to rebuild it, but I haven't seen anything back yet (unless I missed a message in the chain somewhere), so I assume he's still working on it
I doubt it, because he already replied, mentioning the rebuit file that I've already attached the rebuit file to a previous reply.
André