Techman

I think the only limitations you'll face are on the PLM which has a limit of about 1000 links. 

The data for the Zwave, Zmatter, and Zigbee devices is stored on the Zmatter dongle.  The question is if your remove the dongle how will the device tree respond to those devices that are no lonnger accessible. 
If your zmatter board is mounted in the external enclosure You could unplug it and see what happens. I would assume that the device tree would show those devices with a red exclamation mark.
If you mount an already populated zmatter dongle in a different controller the device tree, and associated programs probably won't show the data on the zmatter dongle. I'm not sure if there's a way to do a sync and update.
Probably best to open a ticket 

Clear you java cache, be sure to check all 3 boxes, then download the IoX Launcher from here:
https://isy.universal-devices.com/start.jnlp
You shouldn't be extracting any zip files associated with the ISY
 

There was an earlier firmware version bug that disabled the programs. it has since been fixed.

Probably best to submit a support ticket to see if the bios needs updating / replacing

$39 for two years

If you do a restore device. the link tables in the device will be rewritten with the link tables that are stored in the eisy.
You can check and/or verify your device link tables using the diagnostic option in the device's right click menu
i.e. show device links, after the table populates click on compare. That will compare the links stored in the eisy with the links stored in the device. If there's a link mismatch it will highlighted.

What error are you getting?
Not sure what you mean "upgrade the PLM from OTA"  There are two PLM models, a Serial and a USB. 
Did you follow the "replace PLM procedue"? (see attached file) Note: this is for the ISY994 but is basically the same for the Polisy and EISY
Replace Modem.pdf

If the address is unavailable your other option is to put the device into the linking mode, the controller will then see the address. You can do that without having to remove switch plates.

Why not have a program set variables, one for armed stay and one for armed away.
A program could look at the variables to determine the state of the system, and then reset the variable when the system is disarmed.

In the admin console, after setting the on value you need to click the "on" to the left of the level setting

Being that's it's a brand new product it's possible that the current controller firmware isn't programmed to recognize it.
You should submit a support ticket:  https://www.universal-devices.com/my-tickets

It was most likely the low battery in your motion sensors that caused devices to turn on. I've had that happen..

It's the same display for Aeotec.  In this screen shot the Aeotec firmware version is 1.10
 

You can just ignore the Binary sensor node. Sometimes extra nodes are created depending on the device and the Zwave controller.
I created a folder and move unused nodes into that folder which unclutters the device table.

The Zmatter dongle is powered by the eisy, you don't need an additional power supply

Try doing a factory reset on the switch, then a restore device.
It's also possible that there's a program that has a link to the switch. Take a look at your log to see what's happening at 3:59am

Try deleting the program, then recreating it.
Also verify that the time is set correctly in the admin console

Powercycle didn't help, ticket submitted
 
UPDATE:  Just heard back from UDI, it's a known bug. They expect a fix by the end of the week.

You can recreate the query all program.  Apparently, it doesn't migrate over.
IF
    Time is 3:00AM
Then
     Set ISY Query
Some programs don't migrate over completely, so you'll have a line of code that needs to be manually updated. If you're still having issues with a particular program post a copy of it the forum and we'll try to debug it for you.
 

The IoX Launcher supports Java 8. It may not support OpenJava (OpenJDK)
You can try clearing your java cache and downloading the IoX Launcher again
    https://isy.universal-devices.com/start.jnlp

@jdlugosh
The information you're looking for is towards the bottom of this manual.
2334-2222 Keypad Dimmer manual.pdf

Your program will only run if the time is exactly 9:00 pm and the light is switched on at exactly that time.
Change the first line to  Basement Lights STATUS IS ON
 

There's no option to make that change. Maybe in a future firmware update.

This is how it should be written..  An else statement will only run if the IF statement is false.
IF
   Status 'Second Floor / Bathroom Fan' is On
Then
   Wait 5 minutes
    Set 'Second Floor / Bathroom Fan' Off
Else