Would you mind emailing me file1a and file1b assuming you are willing to share them? Send to: m (at) zorinaq.con
It's possible to have a scenario where your synchronization process (involving Google Cloud?) somehow changed the modification time of your files so that both copies in src/ and dst/ have the same timestamp, in that case rsync will not notice they are different (if they also have the same size). Like the other reply said you have to use rsync --checksum or -c to force rsync to compare the content of files.
As noted in a sibling comment, you should check out the --checkout / -c option. Specifically, replace:
1. rsync -acv src/ dest/
It will be much slower - using lots of cpu and disk access - but more thorough.
>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.
[All three pairs match MD5]4. run rsync - no difference still
5.compare difference by diff - shows gibberish. All three copies open by pdf viewers. The qpdf option doesn't make sense because all the 3 happen to be advanced math textbooks, and the plaintext is impossible to read.
In fact I just checked now, and the same error pattern persists. Its not something I am terribly concerned since I have 3 copies of my data - but this is a pattern which showed up for the first time. I do this exercise regularly (once per month)