Import database from EndNote, but not the linked PDFs

I'm trying to convert from EndNote to Zotero (the standalone version). In my EndNote library each record is linked to a PDF file. However, those PDFs are not part of the EndNote library. Instead, they reside in a special directory, which I update myself. Each EndNote record just contains the related PDF filename (only filename without path, stored in the URL field). This works well (i.e. I can open the PDF from EndNote) provided that the EndNote's "working directory" is the same as the PDF directory. I would like to continue this way with Zotero as well, because the PDF directory is about 3GB in size (and growing), which is too big to sync.

I already managed to import the database using the RIS format, where I modified the EndNote template to include

L1 - `URL|`

The only problem is that Zotero also imports all PDF files into its own directory structure. I would like that Zotero only remembers the path to the PDF, so that I can handle the PDF directory myself, and it should work on all synced computers, even if the path of the PDF directory is not always the same. I noticed that in the preferences one can set base directory for relative path, so it should be possible. But how to do it?
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