After an upgrade to one of the machines linked to my Zotero account, I got errors that some of the attached filed could not be found. Now, I attach most of my files, so I was pretty sure that the files were there. I also double-checked that the base directory was set correctly, and that it was set to relative paths (moreover, only some of the attached PDF were affected, so I knew that the basic setup was OK).
Using Zutilo (a plugin for Zotero), I could figure out that the problem of those attached files was that an absolute path was set. In fact, on the Windows machine (i.e. the machine that was upgraded and where Zotero was set up afresh), I could simply choose to select the file again to resolve the issue, but there were more than a handful of attachments involved.
So I used the Zotero Storage Scanner (another plugin for Zotero). I was useful to read the instructions, as the scanner plugin has no GUI and works in the background to tag broken attachments. On my machine, I got around 1 entry tagged per second, so adjust your expectations accordingly.
Because the scanner plugin tags the attachments/PDF and not the articles, I then created a new collection in Zotero. Selecting the #broken_attachments tag, pressing minus (to collapse all items), I then added all the items to that collection. This way, I was sure to select the entries for the next step.
Selecting all articles with broken attachments, enter Zutilo for the second time. This time, I needed to “Modify attachment paths”. There are two boxes, one after the other. So in the first one, I entered that part of the absolute path, that wasn’t needed (I copied this from Zutilo’s “show attachment paths”), like “D:\ZoteroPDF\” (without quotes). In the second one, I added “attachments:” (without quotes, but including the colon). On my machine, this took around 3 seconds for 2k items.
Because I did the fixes on the GNU/Linux machine (this will also apply to Mac), I used Zutilo once again to modify attachment paths: In the first box, I entered the backslash (“\” without quotes), and made sure to tick “change all instances”, and then in the second box I entered the forward slash (“/” without quotes).
Getting everything synced on the Zotero servers took a while, but all my attachments work again as they should.