Does modifying an access file copy affect original file?
No, modifying a backup file will not affect the original. Access databases are self-contained in the MDB file.

Your statement "Since both files will be pointing to the same database" is incorrect. While both files are identical at the time of copying, they are (for all intents and purposes) separate databases.

If you're pointing an Access application to an external data source (e.g. SQL Server), this does not hold true.