Have been seeking a solution to 'legacy' files - one of the 'discovered' after affects of migrating a 1.9 upwards to the 2 series (many moons ago). Site has legacy turned on courses have legacy turned on ... all files in those courses have 'legacy' designations.
Am almost willing to bet that at some point in time in the future, 'legacy' support will disappear.
So ... go into the course that you just fixed with the search and replace.
Is legacy turned on?
If you turn off legacy in that course do all links to files work?
If not, turn legacy back on.
Then take a gander at:
https://moodle.org/mod/forum/discuss.php?d=350435&parent=1414497
'spirit of sharing', Ken