To fix this is fairly simple. First you will need at least 90 GBs free on you drive where these episodes are located. (or enough to do a season at a time), and you will need MKVToolNix to get "MKVMERGE.exe".



Make a new folder.
Copy all episodes from S03-S09 + Movie to this folder. (or do one season at a time as this will eat a lot of space.)
Make a New .bat file
Copy this code and paste in the batch file.
@ECHO OFF

rem Please enter the full filepath to mkvmerge.exe below without quotes or spaces
rem EXAMPLE: F:\mkvtoolnix\mkvmerge.exe
set MKVMERGELOCATION=

FOR %%A IN (*.mkv) DO "%MKVMERGELOCATION%" --output ".\Fixed\%%A" --aspect-ratio 0:16/9 "%%A"

ECHO ...
ECHO ..
ECHO .
ECHO DONE CHANGING ASPECT RATIO TO 16:9.
PAUSE

On line 5 paste the location to where you may have MKVMERGE.exe located on your computer. If you don't have it, it's a free download, just google it.
Save and run the batch file.
New fixed episode will be saved in a new folder named "Fixed" where the original episodes are located.
Running the batch file may take a while if you're doing all episodes at once. You could split it up and do season at a time as long as they're in separate folders and you just move the batch file.