I've experienced an issue, where links to pdfs (but not .org ) files
do not work in an exported pdf file due to incorrect link syntax, if
the linked pdf is not in the same subtree as the org file that is
exported. If one looks in the .tex file one can see that links to
"outside" *.org files and *.pdf files look the same, but after the pdf
conversion this is not true anymore. I'm therefore not sure where this
problem comes from org-mode or the pdf conversion.
However the issue can be solved by forcing relative links also for
outside directories by setting (setq org-link-file-path-type 'relative).
The following jpg. shows the relevant behavior.
I'm not sure whether relative links could be a problem at one point,
but "adaptive" links to pdfs don't seem to work properly in file trees
outside the org file directory.