For deploying the firmware use the Teensy Loader tool provided by PJRC on their web site. PJRC provides both a graphical and command line version for Windows, OS X and Linux. With the command line version, run the command:
teensy_loader_cli --mcu=imxrt1062 -v -w TEENSY40-<date_version_tag>.hex
or for Teensy 4.1:
teensy_loader_cli --mcu=imxrt1062 -v -w TEENSY41-<date_version_tag>.hex
Instead of imxrt1062 with the --mcu option, you can as well use the board specific names TEENSY40, TEENSY41 or TEENSY_MICROMOD. When loading the firmware the PJRC boot loader will erase the board file system.
Note: If the Teensy board is equipped with Teensy bootloader v1.07 and up, the first attempt to upload the firmware may fail. In that case try again.