If I install High Sierra will it change the file system to APFS, and re-write the firmware/roms?

The High sierra installer will only change the file system to APFS if the drive being installed onto is internal to the Mac, and is an SSD. Otherwise, it will be untouched.

If you have an SSD installed on the Mac Mini, you can force the installer to not convert to APFS if you want to by using the command line tool. See here: https://blog.macsales.com/42884-is-it-possible-not-to-convert-to-apfs-when-upgrading-to-high-sierra/

The APFS conversation is exclusively for the hard drive's file system format. Is has nothing to do with firmware or roms of any type.

It does not affect the general functionality of the Mac in any way.

icwvx wrote:

If I install High Sierra will it change the file system to APFS from HFS, and re-write the firmware/roms?

Installing macOS 10.13 will update the system's firmware.

I read that if a machine has Mojave 10.14 and one wants to return to ElCapitan/Sierra one needs to use an installer rather than erase and clone

If you use an app such as Carbon Copy Cloner you can clone the a High Sierra system back to either an HFS+ or APFS volume. CCC basically just performs a file copy operation to whatever volume you select.

While it doesn't apply to your 2011 Mini, Mojave and High Sierra do not require an APFS file system to work properly, however, macOS 10.15+ does require an APFS file system on the boot drive.

The High Sierra update would update the firmware to the current version for High Sierra whether or not APFS is applied.

Firmware updates and hd file system formats are not related.

Its possible the update will fix that. No harm in trying.

Worst case scenario, you may need to simply wipe the Mac and reinstall the macOs from scratch. Whether its el Capitan, or High Sierra.

Your Mac should be able to boot from Internet recovery to reinstall the OS.

See here: How to reinstall macOS from macOS Recovery - Apple Support