Too tired to fully understand the thread, but I had the same issue I think. (Modem just gone from NetworkManager gui options and ModemManager). Please try "nmcli radio wwan on" in terminal, then just "nmcli radio wwan" to see if its enabled (takes some time). This fixed it for me.
Edit: I have found another scenario in which the modem is unusuable and I think I know how to reproduce/fix it. May post here later if I figure it out.
2nd Edit: I think I figured out 1 issue that may or may not be the cause. Turning the device off and immediately on (At least for my US 4G Pyra) causes several error messages in the kernel buffer/dmesg output that say:
ehci-omap 4a064c00.ehci: port 2 reset error -110
repeated several times followed by:
usb usb1-port2: Cannot enable. Maybe the USB cable is bad?
Googling the error number -110 reveals something wrong with usb device resume after a suspend, and recommended waiting 5 minutes before turning back on what device (server, laptop, etc) you have.
So basically the following is my ritual to bring back the modem:
1. nmcli radio wwan off
2. Turn the pyra off
3.
*Listen to this to pass the time*
4. Turn the pyra on
5. nmcli radio wwan on
6. Wait 1 minute
It works.
Further googling reveals a miriad of omap ehci initialization issues so I share with you what I think is the most likely candidate because:
1. It mentions running "usb start" during uboot which the pyra uboot does
2. It mentions the fix causing a regression in OMAP 5
I am not a developer/programmer and have no idea what that commit/patch does so this post may be little more trustworthy than gas station bathroom graffiti.
OMAP EHCI issue link:
https://marc.info/?l=linux-usb&m=134098423528415&w=2