I don't see why the link would break. Can you describe what you have set up and what you are doing in more detail?
How did you open the stored file? Did you go directly to the folder where the file is stored and modify the file by opening it from there?
If so, that would explain what you have experienced.
You can use Export Field Contents to open the file and then re-insert the modified copy in order to change it.
Or you might try using the GetThumbNail function to set the container field to a downsampled copy of the file to reduce the image resolution to a smaller resolution. (Try this on a copy so that you don't mess something up if it doesn't work).
But I thought externally stored files--due to storing a file reference weren't supposed to result in a major file increase due to inserting large picture files into those container fields with external storage specified.
Wonder what would happen to your file size if you left your files unmodified and did this instead:
Save a clone (no records) of your file.
Import all records from all tables into the clone
Compare file sizes between this new copy of your file and the original. Others have reported major changes in file size from this.