What does 'changed URL to new one" mean? The PDF is outside Moodle file system and you have a link directly to the PDF? If that's the case, it could be true ... corrupted file. Did you upload via binary? Did you change the name of the file slightly from the old name?
As far as Certificates ... the certificate mod in 1.9 used a file system that was conventional for that version. After your first jump from 1.9 to 2.2 did you check out changes to the moodledata directory?
Seems I recall helping someone migrate a 1.9 to a 2.x there were still course ID folders in the data directory ... mod, some ID number, and drilling down eventually one got to a certificate PDF files.
Have you updated the certificate mod? Compat version for M2?
On a site using certificate mod it shows the version is:
2013102300
links to certificate mod show this:
siteurl/mod/certificate/view.php?id=5074
The buttons link to:
siteurl/mod/certificate/view.php?id=5074&action=get
In config of the cert there are issue options:
Delivery set to what? Open in New Window? Try re-setting to force download.
Help for that says:
Choose here how you would like your students to get their certificate. Open in Browser: Opens the certificate in a new browser window. Force Download: Opens the browser file download window. Email Certificate: Choosing this option sends the certificate to the student as an email attachment. After a user receives their certificate, if they click on the certificate link from the course homepage, they will see the date they received their certificate and will be able to review their received certificate.
Save certificates?
It also had Design options.
If I recall correctly the old mod had in it's mod directory a pix directory which is where that version held the seals, signatures, border, etc.
Is that directory still there?
Does your apache error log say/show anything related to those PDF links?
'spirit of sharing', Ken