The solution you're reaching for, a template that compares three lists and flags missing files, is the right instinct, but the tools you're describing will only get you part of the way there. You're already thinking in terms of unique identifiers and conditional checks, which is exactly where you need to be. The real question isn't whether you can build this template; it's whether you should have to build it at all.
Let's be direct about what's happening here. Someone else attempted this audit before you, deleted a heap of files, and now you're working with a restore. That means you're not just comparing data, you're verifying that a recovery actually worked. That's a fundamentally different task than a standard audit, and it demands a method that doesn't introduce new opportunities for error. Your current plan to export a PDF from the online portal is a bottleneck waiting to happen. PDFs are for reading, not for processing. You'll spend more time cleaning that data than you will comparing it.
Instead, consider this: export the online list as a plain text file or CSV if the portal allows it. If it only offers PDF, use a simple extraction tool, Power Query in Excel can pull tables from PDFs directly, no manual typing required. Then, load all three lists into a single workbook. Use UNIQUE to build a master list of every file name across all locations, then use COUNTIF or XLOOKUP to check each location's presence. Your table idea works, but drop the "VTSACK" typo, VSTACK is the function you want, and it will stack your lists vertically so you can deduplicate them in one step. You're close to a working solution; you just need the right sequence of functions.
What this really reveals is the fragility of manual file management at scale. You're doing the work of a database with a spreadsheet and a command prompt, and it's working only because you're disciplined enough to plan it out. But the system itself isn't helping you. If your organization is relying on three separate locations with no automated reconciliation, that's the underlying problem. Your template is a patch, not a fix. The practical takeaway is this: build the template for today, but document the process thoroughly enough that someone else, or an automated script, can run it next time. Your audit should leave the file structure more reliable than you found it, not just checked off a list.