Rather than manually re-establishing the links, I decided to look into a more automated solution and I was fortunately able to find one! I document it below in case I, or others, need to do this again. However, all of the links are broken, which is a major issue. My bibliography entries in Zotero have the links still associated with them and my PDFs are in the same absolute path as my last computer. I am currently migrating to a new computer and am able to sync down my Zotero bibliography into the Zotero app and my PDF library to my local folder. I currently keep my PDFs in a local Box directory that is synced with the cloud, so I can easily view my files through Zotero locally and also retrieve them from anywhere later through the internet. The wonderful plugin ZotFile can be used to automatically rename and organize PDF files in a custom way and to link bibliography entries with PDFs stored in arbitrary locations, making it useful for storing your PDF library in a custom location. I highly recommend it because it does a great job with storing bibliography, has plugins to automatically download bibliographic info and PDFs in Chrome and to insert citations in MS Word, and because it is open source! Bibliography entries can by synced with Zotero for free (to a limit), making them accessible anywhere through the internet. For the past couple of years, I have used Zotero to manage my bibliography.
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