So to avoid saving changes to the "wrong" project, is it as simple as closing the original project and opening the one AE created when it ran the Collect Files command?
Yes, but generally there is little or no reason to use the command in this manner, if you already obey a clean working style, that is create a dedicated folder structure for each project. After all, that is pretty much what the comamnd does - convert all absolute file paths into relative ones and put them into a nice folder. As for the other things - never ever work off external drives unless they are quality Firewire or eSATA RAIDS. There's simply too many things that can go wrong. The drives could lose connection or go into suspend mode, they could overheat and last not least, their fragile nature will make them susceptiple to any kind of mechanical failure, be it due to random tremors damaging the disk or your cat taking a liking to the losely plugged in power chord...
Thanks for your reply. I'm afraid I didn't make it clear why I was looking at Collect Files in the first place. But reading your answer has helped me decide; transferring 100G of assets shouldn't take more than an hour and I can spare that.
Now - on to the other setup questions... a new thread is probably appropriate so I'll mark this "answered" and thank you again for your reply.