Welcome!
Do run a search on the forum for “academic” or perhaps “researcher”. Workflows have been discussed many times and are always interesting to read about.
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“DT” isn’t a separate drive so this question is redundant. DT files are stored locally on your Mac, and synced to your iPad.
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I’m ignoring the second part of your question because we’ve agreed in question 1 you’re storing your files in DevonThink on your Mac. When you open a PDF from DTTG into PDF Expert changes should sync back automatically. With the caveat that it isn’t working quite properly at present but will be resolved (see here). This is fine for what you want - if you ever need a clean version of the PDF again, you can export a clean version from DT on your Mac without annotations.
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I think on both Mac and iPad you would use the DT item link (on Mac you certainly would, I’m just not sure how it works on DTTG and your question isn’t clear as to which device you’re using for this step). Are you a new user of Obsidian too? If so, do think about if you actually need/want this step. Plenty of people do use DT and Obsidian together, but equally plenty of people don’t. I just store my notes in DT alongside my research material. I tried Obsidian but it’s much easier just having all my work in one place.
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I will leave this to others, but you can also run a search in the forum for Zotero as various folk use it.