I am having a similar issue with Jurassic Park Premium, only 3 switches are not working and they also connected to CN12. The game was perfectly fine! and all and all of the sudden these switches stopped working.

I understand we have different games but the issue seems the same. My switches are connected to NODE 8, CN12.

Could this be a software issue, something automatically refreshed on the backend by the new Stern Connect? I find this issue odd! Especially when my game was perfectly fine!

Edit found my issue: there was a break in the EOS switch by the upper flipper.
Need to solder it back up and we are back in business.

Here is how I found my issue:
Take a look at the switch reference manual and identify the switches, if they all belong to the same connector then you are on track to fix it how I did.
The switches have 2 wires, one is power I guess and the other is ground. Power goes straight from the connector to the switch, ground does not, and it jumps from one switch to the next from the node board-->connector-->switches in that connector.
They all share the same ground cable.

In my case, CN12 was black-red ground, so I checked all the switches on that connector (only 8 or 9 switches to check) until I found a broken/disconnected ground wire. It was the EOS at the upper flipper.

Hope that helps!

Alternatively, you can use this to troubleshoot, which is probably a lot more appropriate:

https://sternpinball.com/wp-content/uploads/2020/11/SPIKE-System-Manual.pdf

Page 37 has all the processes to diagnose the switches. It is actually quite easily now that I know what the correct process is.

Good luck!