Hi, I downloaded a bunch of EPUBs from Archive of Our Own and deleted them from iFiles some years ago. They’re no longer available for download and I would like to transfer them from iBooks to my PC. Anyone know of a reputable (read: virus-free lol) way to do this? My ultimate goal is to load them into Calibre like I do all my books nowadays.
It's not clear to me from your description where these books you want to transfer reside.
They’re EPUB files in the iBooks Application on my iPad Pro/iPhone.
Okay. I would just turn on iCloud Drive Sync (Books settings) and make sure Books has iCloud storage turned on (iCloud settings).

At this point, you might need a Mac to get your files.

What I do on my Mac is to search for one of the ePub files using Finder. The path information shows 'iCloud Drive > Books > myBook.epub'. I bring up the context menu and choose Show in Enclosing Folder. This opens a Finder window that display all of the Books documents stored in iCloud, with a 'cloud' icon that shows they are not downloaded. Click, and they download.

Now I can drag them out of the Books folder and put them anywhere to use them. Obviously most purchases from Apple will have DRM to deal with, but that won't apply to your personal ePub books.

There is an iCloud client for Windows (from Microsoft Store) but it probably does not support the above scenario (I am curious enough to try it, once my old Windows 10 box -- which I haven't turned on for months -- finishes with updates and I can install the client).

Even on Mac, if you open the iCloud Drive folder, you won't see a Books folder there to navigate to. Yet when the Books folder is open, it shows iCloud Drive as the parent folder. Is there way to copy using Terminal, etc.? Don't know yet.

I thought there would some way to access Books storage with Finder when the device is connected to the Mac (via USB or wirelessly) with Finder (on Windows you would need iTunes app). But if so, I can't figure out how to do it. There is a Manage Storage option that lets you delete content from Books. And there is Sync option, but where is the location on Mac it syncs to? I don't know.

In summary, you can definitely get them from iCloud if you have a Mac.
I technically have an old 2008 MacBook Pro, but the last software update available doesn't include iBooks support (If we're talking about the ability to read books on mac, if the iCloud files for iBooks can still be accessed without that functionality then I should be able to.) I will admit however that I'm scared to turn it on and sync it. It was connected to my iCloud files account once upon a time and I'm afraid it will wipe things away in its efforts to sync. Did you happen to find anything about the Windows route before I try?
I have a 2009 MacBook Pro which like yours is stuck on an older version of macOS. I'll see if it will work. It still runs great (replaced the fan, put in SSD drive, replaced the battery...) but at this point probably better to install Linux or Windows 10 on it to have something that gets updates.

I did install iCloud on my Windows system, I think, but haven't had a chance to see if that will work. I give it about a 2% chance.
Another thing is do not purchase DRM free ePub from Apple. Purchase from Kobo or eBooks.com and you won't have this problem in the future.
Thank you. Please let me know about the mac. In the mean time I'm using a set of external hard drives to back up my iCloud account and then I'm going to try to sync up my MacBook Pro.
I could not get it to work on my vintage Mac. iBooks (as it was then known) does not seem to interoperate with iCloud documents for Books running more current macOS.

I installed iCloud Drive on Windows but didn't see any obvious way of getting Books 'user documents'. It's just for sharing files and photos (and also share web site passwords via Microsoft Edge plugin Apple developed).

And it seems you can download, evict, and copy iCloud documents (including Books 'user documents') using command line.

The folder for Books user documents is

/Users/[user name]/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents

(This same folder exists on El Capitan but it was empty, so apparently it is no longer supported on server side.)

(I suppose you can also copy files to this folder and iCloud daemon will upload them? Seems like it could be a simple calibre plugin to manage Apple Books content that is user-supplied.)

and the tool to control iCloud daemon download and un-download is called brctl.

'man brctl' will show the options.

https://apple.stackexchange.com/questions/328329/is-there-a-way-via-the-command-line-to-cause-icloud-files-to-download

Note that ePub files are represented in iCloud as folders, just as if you had 'exploded' it. So in addition to copying, you need to have script to re-constitute it as an ePub file (with contents in the expected order).

As to @JSWolf's point, this folder only contains user content. Yet deDRM refers to another tool that can 'liberate' purchases from Apple Books but I don't know the current status of that tool or how it manages to work. I've made only a handful of such purchases (mostly just free things like user guides for Apple devices, developer documentation etc.), so it is not something I'm particularly curious about.

But I agree (even assuming it is possible) that it is probably more trouble than it is worth, especially for content that doesn't have DRM in the first place.
They didn't purchase the stories, they downloaded fanfic to the iBook app. Now, the original stories were pulled from the archive, so they can't be downloaded again. They don't want to lose them.