Comparing each item from dir with each item from another dir
It's recommended to use enumerate rather than iter (renamed i), _ and indexing.

for i, abs_path in enemerate(mentors_sql_abs):
    mentors_sql[i][0] = abs_path

It's better to use zip rather than build mentors_sql manually.
Your function could further be simplified if you don't extend mentors_sql_* and just yield the values.
Please only use one string delimiter, either ' or ".
x is a pretty bad variable name, I would use file. Even for a comprehension it's pretty poor, as x isn't short hand for anything.
The only difference between the two functions as you walk different paths. And so you can change your input to account for this, and use one function.
I don't see the need for returning both relative and absolute paths, and so won't comment on it too much. You may want to return one and convert when needed.


def find_sql(path):
    for dirpath, subdirs, files in walk(path):
        for file in files:
            if file.endswith('.sql'):
                yield (
                    path.join(dirpath, file),
                    path.join(path.basename(dirpath), file)
                )


mentors = find_sql(config["MAIN_DIR"] + '\\Homework')
students = find_sql(config["MAIN_DIR"] + '\\Students Homework')