I’ve run into exactly the same issue with my large ttrpg ebook/pdf collection (+100k file data hoarding… it’s not a problem, I swear) and I’ve not really found a good option I’m entirely happy with. Calibre duplicates everything and I don’t like the thought of having my collection’s organization tied to a specific piece of software if I just delete my duplicates. Plus I’m elitist and think the UI/logo are gross to look at.

Zotero is the least worst option I’ve found, but it’s geared towards scholarly journals and such, so not great, but serviceable. Not sure if it’s on linux though.

Jellyfin is apparently able to handle ebooks with a plugin, though I didn’t particularly care for it when I tried it months ago.

There’s a handful of other ebook software out there, mostly geared towards comics/manga, so depending on what you have those might be worth looking for.

I’d like to use Obsidian for it and just turn the directory into a vault and let it automatically scan the folders for files, but that doesn’t work great either.

The best piece of software I’ve seen that could potentially handle it is an app called Stashapp… which is unfortunately geared towards adult film. But it’s feature-set if it could be applied to PDFs seems like it would be ideal.

I used Win10 mostly without issue and when I transitioned to Win11 that went without issue as well and it’s been pretty much smooth sailing the whole time. The few annoyances I had with it, I was able to find something that fixed the issue, it just works. The only thing I really didn’t like was that the only reason I transitioned to Win11 as early as I did was because of an update they sent out that made it sound at the time like I had to switch over, something about the wording made it seem like I had no choice, I remember it being a bit confusingly worded. I had wanted to hold out as long as possible on Win10, but because of that went ahead with the switch. It’s been fine since then, but I would’ve preferred not having to switch because of that.

I have encountered this issue before when I tried using Obsidian my RPG pdf collection (10,000s of files), would not recommend. I do still like Obsidian and will keep using it, but would something like Trillium work as a sort of PDF library software for a massive amount of files like that? The main need is to be able sort/categorize game systems using tags, link to pdfs, and maybe have some sort of Dataview-esque query capabilities. Zotero is the least worst option, but it still has some annoyances for me and I’ve still been looking for something that could help me organize better. I know this is billed as a note-taking app, so it’s a weird use-case, but Obsidian was pretty close to being a decent solution, if not for the slow speed issues.