pgloader will keep a separate file of rejected data, but continue trying to copy good data in your database.
pgloader also implements data reformatting, a typical example of that being the transformation of MySQL datestamps 0000-00-00 and 0000-00-00 00:00:00 to PostgreSQL NULL value
You can force Git to detect the history of the copied file:
Instead of copying, switch to a new branch and move the file to its new location there.
Switch to the original branch and rename the file.
Merge the new branch into the original branch, resolving the trivial conflict by keeping both files.
Restore the original filename in a separate commit.