At least my version of this bug (see other thread: Incomplete sync in DTTG3?) has nothing to do with opening the PDF files. DTTG3 was already listing the files in question as “0 pages” before I opened them. Also, I rarely annotate PDF files in any way, and definitely hadn’t annotated the ones showing the problem.
Now, it’s possible that there are two related bugs with similar symptoms, as my version also doesn’t appear to affect any other copies of the database.