Earlier quoted context omitted.
If your PDF files have the same MD5 checksum but "diff" shows differences then this is an MD5 collision. Maybe it's a trivial thing, eg. your 3 files got resynchronized right between running rsync and running diff. So you should have retried rsync after the diff. Or you obtained these PDFs from a source that purports to demonstrate MD5 collisions. Or someone is attacking you by replacing your files. Or, more likely,…
I tried and the difference between the two turns out all gibberish. >Or, more likely, this is user error, and you are not reporting to us what's happening exactly. Here's the sequence: 1. rsync -av src/ dest/ 2. diff -r src/ dest/ [Shows 3 pairs of differences] 3. md5 file1a & file 1b; compare md5 file2a & file 2b; compare md5 file3a & file 3b; compare [All three pairs match MD5] 4. run rsync - no difference still 5.…
1. rsync -acv src/ dest/
It will be much slower - using lots of cpu and disk access - but more thorough.