I have no real idea of what happens. You may try some of the following, to try to understand the cause of the problem:
- do you have the same problem from each mac? For the same files?
- if you copy a "missed" file to a local folder, and index this folder, can the file be found?
- if you remove the tags from one file, then update the index, can it then be found?
- if you add such a tag to a file that can be found, then update the index, can you still find it?
- can you find the files by searching:
[all items of type] [PDF]
in: [the folder containing them]
- What is the filesystem of your "macServer"? APFS, HFS, other? Case sensitive? What is the sharing protocol (AFP? SMB? other?)
- are there some other particularities for these files? maybe an uppercase .PDF extension? Non ascii characters in the name? Do they have an HFS type/creator?
- maybe a screenshot of your query, of the result, and of the folder in the Finder could also help.
Thanks