no it won't. Generally they are preserved. The models may be removed if you try to upgrade more than one major version on the radio.
The Factory reset command on the Version page since 2.1.X removes all models and sets the Radio settings including the calibration to the default values. In particular it will set Mode 1 in the radio settings. If your sticks are configured as Mode 2 (Throttlle on the left) then you willl have some strangeness until you set the mode configuration correctly so the sticks an radio settings agree. Note that it may also set the default channel order (for new models) to RETA...I recommend using AETR since that order is assumed by various things (FrSky's S receivers and the FrSky version of the Multimodule) You will also need to re-calibrate the sticks and pots.
Note: You can also wipe out all the models by writing your own .otx file to the radio using OpenTX Companion's write models and settings command. Be aware that this will overwrite the Radio Settings also and you will need to re-calibrate the sticks and pots after doing this. After writing the models and settings read the .otx back into Companion before updating the models again so you write the correct settings back out.
I have just checked the VERSION page and it says 126.96.36.199 and does not have a reset option (MENU long backs up the EEPROM). I'm sure I have seen V2.1.6 on another page though?
I did download Companion9x but when I try to read the EEPROM I get an error message
"avrdude.exe: error: could not find USB device "USBasp" with vid=0x16c0 pid=0x5dc"
So I can not reset or upload anything new.
On the X9D if you push the lower trim switches inwards and switch on it invokes the Taranis bootloader. I have used the Companion to manually get rid of the logical switches and special functions. I need to read more of the OpenTx manual.