Upgrade StorageLocal Storage of Manually-Downloaded PDFs on New PC
When Google Scholar articles do not automatically download as a PDF (using the Google extension), I manually save each PDF in my Zotero\Storage folder, which I've been doing on my laptop for the past year. I also use Zotero's sync to the cloud feature. I just noticed on my new PC (that syncs to my Zotero cloud account) all of these "manually-downloaded" PDFs on my laptop have been moved into their own folders on my new PC. Is there a help page that explains this because I use hyperlinks to get to my articles and now I have two different hyperlinks for each of these manually-downloaded articles (the link on my laptop is different than on my PC).
Q: "all of these "manually-downloaded" PDFs on my laptop have been moved into their own folders on my new PC"
A: Most of my PDFs save automatically into folders created by Zotero when using the Google extension. But when the Google extension will not download the PDF (usually due to permissioning issues), the only thing that saves is the article summary. So I manually find the PDF through my library and then save to the Zotero "Storage" folder. Of the approximately 50 PDFs I've had to manually save, they are all stored at the root level of the "Storage" folder. But after I sync to the cloud and then set up a new PC which pulls everything down from the Zotero cloud, it puts each of these PDFs in their respective folders.
Q:"I use hyperlinks to get to my articles"
A: I keep all of my articles listed in Excel, with links to the PDF file, but there is now a difference between the PDF location on my laptop and PC because on my laptop the manually-downloaded PDFs are saved in the root folder while on my PC they are stored in sub-folders specific to the article.
And I think you're both leaving something out and misunderstanding what's actually happening. You don't say it, but presumably after saving those files to the 'storage' root, you're also actually adding them to Zotero (or else they wouldn't be synced). And when you add them to Zotero, Zotero copies them into their own folders, there, on that computer, as it would with any other file you add to Zotero as a stored file, and leaves the original in place, completely unreferenced by Zotero. (Linked files remain referenced, but they also don't sync, so that's not what you're doing.) So the fact that they show up in subfolders on the other computers is sort of beside the point. If you do a "Show File" on the files on the first computer, you'll see that where they actually exist, as far as Zotero is concerned, is in the subfolder.
So at this point, you can just delete the files in the 'storage' root, since those already exist in Zotero in their 'storage' subfolders. Going forward, if a PDF isn't saved and you want to add it, you should either 1) click the "Save to Zotero" button while viewing the PDF in your browser (which is the browser default) and then drag the PDF item on top of the regular item, thus skipping creation of an initial local file altogether or 2) save the PDF (if you don't view PDFs in the browser) and drag it from the download folder onto the item in Zotero, and then delete the downloaded file. Since you're using stored files in Zotero, the original location of the file on disk is irrelevant, and the original file should be deleted.
I'm not sure why you would keep a list of PDFs in Excel when you have them in Zotero — that seems like a duplication of work that Zotero does for you — but if you really want to do that for some reason, you would want to store the actual path to the file in Zotero, which you can see via Show File.
And definitely stop making manual changes in the data directory. The whole point of using stored files is that Zotero manages the files for you.
Separately, I'm not actually saving the URLs to Excel but I didn't want to overcomplicate my question above. I'm actually saving them to a database in "TheBrain" which is a mind-mapping program. It allows me to visually link articles to one another, which I find incredibly useful (it would be great if Zotero would interoperate with their program because for now, the process of getting my Zotero data into their database is manual and doesn't sync). Having the article's local folder URL in TheBrain database allows me to simply click an item and the PDF opens).