Automator: is "selective" sync possible?

Hi, everybody!
Hope you can help me solving this problem.
Here's the scenario: I own an external HDD in which I have all my docs (yes: it's regularly backed-up to another external HDD... ), "categorized" in folders-subfolders.
When I need to write and/or make a new Keynote on a topic, I usually plug my HDD into my MacBook, then copy all files I need into a "Documents\Temp" folder, read/annotate/modify all those files in order to make more sense to my research and then put them back.
The way I'm handling this workflow is quite... primitive: I copy files/folders into my Temp dir, then write/paste the path into a TextEdit file, in order to be able to put those files I worked with (and on...) back into their original places.
You can easily understand that this way of work(flow)ing is quite simple if you deal with 5-10 files, but as this number increases the "put-file-back" operation is a real pain.
That's why I was wandering if there is a way to "Automate" this workflow.
Please note:
1. I don't (usually) need all files in a subfolder, nor do I need whole folder(s) and subfolder(s), that's why a simple sync app shouldn't fit my needs.
2. I don't want (better: I can't...) have all my docs in my MacBook, because of space (i.e.: Gigabits...) reasons.
3. Most times I can trash many of the files I copied, because they are unmodified (i.e. I use them as a reference), but there's always a few (say: 10-20) files that are modified. And of course I don't want to loose those changes.
4. Finally: no, I don't want to simply carry my external HDD...
Is there someone that could help me finding a solution? I wrote "Automator" because I think it's strong enough to do this kind of job. But if anyone knows an app that exactly does what I need, please let me know.
Thanks!

Michael
Thanks for your question, that clarified it. One more question: when I add a new song or album to iTunes, it appears on my iCloud devices (iPhone, iPad), but I need to download the content (i.e. the songs) manually by tapping on the cloud symbol. I guess there's no setting for automatically download all songs synced to the cloud (I guess that would kind of contradict what you wrote, right)?

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